As filed with the Securities and Exchange Commission on
February 2, 2006
                  Registration No. 333-______________________

                          UNITED STATES
               SECURITIES AND EXCHANGE COMMISSION
                     WASHINGTON, D.C. 20549
- -----------------------------------------------------------------

                            FORM S-8
         REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF
                             1933
- -----------------------------------------------------------------

                  PATRIOT TRANSPORTATION HOLDING, INC.

     FLORIDA                                           59-2924957
     (State or other jurisdiction                 (I.R.S. Employer
     of incorporation or organization)          Identification No.)

     1801 Art Museum Drive
     Jacksonville, Florida                           32207
     (Address of principal executive offices)     (Zip code)
- -----------------------------------------------------------------


                 PATRIOT TRANSPORTATION HOLDING, INC.
                       2006 STOCK INCENTIVE PLAN
                        (Full title of the plan)
- -----------------------------------------------------------------


                       Ray M. Van Landingham
               Vice President and Chief Financial Officer
                       1801 Art Museum Drive
                     Jacksonville, Florida 32207
             (Name and address of agent for service)
                          904-396-5733
             (Telephone number, including area code,
                      of agent for service)
- -----------------------------------------------------------------

                            Copies to:
                        Daniel B. Nunn, Jr.
                         McGuireWoods LLP
                      50 North Laura Street
                            Suite 3300
                    Jacksonville, Florida 32202
- -----------------------------------------------------------------



                     CALCULATION OF REGISTRATION FEE

- ----------------------   ------------------  ----------  -----------

Title of each class      Amount to be        Proposed     Amount of
of securities 	         Registered (1)      maximum	  registration
to be Registered                             aggregate	  fee
					     offering
                                             price (2)
- ----------------------   ------------------  -----------  ----------

Common Stock, par value  300,000            $ 19,168,500  $2,052.00
$.10 value per share
(including preferred
share purchase
rights)
======================   ==================  ============ ==========

  (1)  Pursuant to Rule 416 under the Securities Act of 1933, as
       amended, this registration statement also covers additional
       shares that may become issuable under the plans by reason of
       certain corporate transactions or events, including any stock
       dividend, stock split, recapitalization or any other similar
       transaction effected without the receipt of consideration which
       results in an increase in the number of the registrant's
       outstanding shares of common stock.

  (2)  Estimated solely for the purpose of determining the
       registration fee pursuant to Rule 457(h) under the Securities Act
       of 1933 based upon the average of the high and low sale price of
       Patriot common stock as reported by NASDAQ on January 31, 2006.

                             EXPLANATORY NOTE
			     ________________

     This registration statement registers shares of common
stock, par value $0.10 per share (the "Common Stock"), of Patriot
Transportation Holding, Inc. (the "Company") that may be issued
and sold under the Patriot Transportation Holding, Inc. 2006
Stock Incentive Plan (the "Plan").

                                   PART 1
				   ______

         INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS
	 ____________________________________________________

Item 1.     Plan Information.*
_____________________________

Item 2. Registrant Information and Employee Plan Annual
Information.*
_______________________________________________________

*  The documents containing the information specified in Part 1
of Form S-8 will be sent or given to employees as specified by
Rule 428(b)(1) of the Securities Act of 1933, as amended (the
"Securities Act").  Such documents need not be filed with the
Securities and Exchange Commission (the "SEC") either as part of
this registration statement or as prospectuses or prospectus
supplements pursuant to Rule 424 of the Securities Act.  These
documents and the documents incorporated by reference in this
registration statement pursuant to Item 3 of Part II of this
registration statement, taken together, constitute a prospectus
that meets the requirements of Section 10(a) of the Securities
Act.






                                  PART II
				  _______

           INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
	   __________________________________________________

Item 3. Incorporation of Documents by Reference.
_______________________________________________

     The following documents previously filed or to be filed with
the SEC are incorporated by reference in this registration
statement:

          (a)  The Company's Annual Report on Form 10-K for the
fiscal year ended September 30, 2005 (the "Annual Report"); and

          (b)  Other reports filed pursuant to Section 13(a) or
15(d) of the Securities Exchange Act of 1934 as amended (the
"Exchange Act") since the end of the fiscal year covered by the
Annual Report.

     All documents subsequently filed by the Company pursuant to
Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to
the filing of a post-effective amendment to this registration
statement which indicates that all securities offered have been
sold or which deregisters all securities then remaining unsold,
shall be deemed to be incorporated by reference in this
registration statement and to be part hereof from the date of
filing of such documents.

     Any statement contained in a document incorporated or deemed
to be incorporated by reference in this registration statement
shall be deemed to be modified or superseded for purposes of this
registration statement to the extent that a statement contained
in this registration statement, or in any other subsequently
filed document that also is or is deemed to be incorporated by
reference in this registration statement, modifies or supersedes
such prior statement.  Any statement contained in this
registration statement shall be deemed to be modified or
superseded to the extent that a statement contained in a
subsequently filed document that is or is deemed to be
incorporated by reference in this registration statement modifies
or supersedes such prior statement.  Any statement so modified or
superseded shall not be deemed, except as so modified or
superseded, to constitute a part of this registration statement.

Item 4. Description of Securities.
_________________________________

      Articles  III,  VII,  and XIII of the Amended  Articles  of
Incorporation   of  the  Company  previously   filed   with   the
Registration  Statement  on  Form  S-4  (File  No.  33-26115)  as
amended, pursuant to the Articles of Amendment to the Articles of
Incorporation  previously as an exhibit to the Annual  Report  on
Form 10-K for the fiscal year ended September 30, 1994 (File  No.
33-26115)  are  incorporated by reference  in  this  Registration
Statement on Form S-8.

Item 5. Interests of Named Experts and Counsel.
______________________________________________

     Not applicable.

Item 6.  Indemnification of Directors and Officers.
__________________________________________________

     Section 607.0850 of the Florida Business Corporation Act
permits, and in some cases requires, the Registrant as a Florida
corporation to indemnify a director, officer, employee, or agent
of the Registrant, or any person serving at the request of the
Registrant in any such capacity with respect to another entity,
against certain expenses and liabilities incurred as a party to
any proceeding, including, among others,




a proceeding under the Securities Act, brought against such person
by reason of the fact that such person is or was a director,
officer, employee, or agent of the Registrant or is or was serving
in such capacity with respect to another entity at the request of
the Registrant.  With respect to actions, other than in the right
of the Registrant, such indemnification is permitted if such person
acted in good faith and in a manner such person reasonably
believed to be in, or not opposed to, the best interests of the
Registrant, and with respect to any criminal action or
proceeding, if such person had no reasonable cause to believe his
or her conduct was unlawful.  Termination of any such action by
judgment, order, settlement or conviction or a plea of nolo
contedere, or its equivalent shall not, of itself, create a
presumption that such person did not act in good faith and in a
manner he or she reasonably believed to be in, or not opposed to,
the best interest of the Registrant, or with respect to any
criminal action or proceeding, had reasonable cause to believe
that his or her conduct was unlawful.

     With respect to any action threatened, pending or
contemplated in the right of the Registrant to procure a judgment
in its favor against any such person, the Registrant may
indemnify any such person against expenses actually and
reasonably incurred by him or her in connection with the defense
or settlement of such action or suit, including the appeal
thereof, if he or she acted in good faith and in a manner he or
she reasonably believed to be in, or not opposed to, the best
interests of the Registrant, except that no indemnification shall
be made in respect of any claim, issue or matter as to which any
such person shall have been adjudged to be liable for negligence
or misconduct in the performance of his or her duties to the
Registrant unless the court in which the action was brought
determines that despite the adjudication of liability, but in
view of all the circumstances in the case, such person is fairly
and reasonably entitled to indemnity for such expenses.

     Section 607.0850 of the Florida Business Corporation Act
also provides that if any such person has been successful on the
merits or otherwise in defense of any action, suit or proceeding,
whether brought in the right of the Registrant or otherwise, such
person shall be indemnified against expenses actually and
reasonably incurred by him or her in connection therewith.

     If any director or officer does not succeed upon the merits
or otherwise in defense of an action, suit or proceeding, then
unless pursuant to a determination made by a court,
indemnification by the Registrant shall be made only as
authorized in the specific case upon a determination that
indemnification of the director or officer is proper because he
or she has met the applicable standard of conduct.  Any such
determination may be made:

          (a)  by the board of directors by a majority vote of a
quorum consisting of directors who are not parties to such
action, suit or proceeding;

          (b)  if such a quorum is not obtainable, or, even if
obtainable, by a majority vote of a committee duly designated by
the board of directors (in which directors who are parties may
participate) consisting solely of two or more directors not at
the time parties to the proceeding;

          (c)  by independent legal counsel selected by the board
of directors prescribed in paragraph (a) or the committee
prescribed in paragraph (b); or if a quorum of the directors
cannot be obtained for paragraph (a) or the committee cannot be
designated under paragraph (b), selected by a majority vote of
the full board of directors (in which directors who are parties
may participate); or

          (d)  by the shareholders by a majority vote of a quorum
consisting of shareholders who were not parties to the proceeding
or, if no such quorum is obtainable, by a majority vote of
shareholders who were not parties to such proceeding.




     Section 607.0850 of the Florida Business Corporation Act
also contains a provision authorizing corporations to purchase
and maintain liability insurance on behalf of its directors and
officers.  The Registrant maintains an insurance policy which
insures directors and officers of the Registrant against amounts
the directors or officers are obligated to pay in respect of
their respective legal liability, whether actual or asserted, for
any negligent act, any error, any omission or any breach of duty
which, subject to the applicable limits and terms of the policy,
includes damages, judgments, settlements, costs of investigation,
and costs, charges and expenses incurred in the defense of
actions, suits or proceedings or appeals thereto, subject to the
exceptions, limitations and conditions set forth in the policy.

     The Articles of Incorporation of the Company provide for
indemnification of its officers and directors, in their capacity
as such, in accordance with the laws of the State of Florida.

     Article X of the Articles of Incorporation of Patriot
Transportation Holding, Inc., provides as follows:

     "1.  The corporation shall indemnify and hold harmless each
person, his heirs, executors and administrators, who shall serve
at any time as a director or officer of the corporation or, at
its request, of any other corporation, partnership, joint
venture, trust, or other enterprise, from and against any and all
claims and liabilities to which such person shall become subject
by reason of his being or having heretofore or hereafter been a
director or officer of the corporation, or of any other such
corporation, partnership, joint venture, trust or other
enterprise, or by reason of any action alleged to have been
heretofore or hereafter taken or omitted by such person as such
director or officer, such indemnification to be in accordance
with the laws of the State of Florida as now in existence or as
hereafter amended.

     2.   The corporation shall have the power to purchase and
maintain insurance on behalf of any person who is or was a
director or officer of the corporation, or is or was serving at
the request of the corporation as a director or officer of
another corporation, partnership, joint venture, trust, or other
enterprise, against any liability asserted against him and
incurred by him in any such capacity, or arising out of his
status as such, whether or not the corporation would have the
power to indemnify him against such liability.

     3.   The corporation, its directors, officers, employees and
agent shall be fully protected in taking any action or making any
payment under this Article X or refusing to do so, in reliance
upon the advice of counsel.

     4.   In addition to the foregoing provisions, this
corporation shall indemnify each person or party described in
paragraph A of this Article X to the fullest extent permitted by
Section 607.014, Florida Statutes.

     5.   If any part of this Article X shall be found in any
proceeding to be invalid or ineffective, the remaining provisions
shall not be affected."

Item 7.  Exemption from Registration Claimed.
____________________________________________

     Not applicable.







Item 8.  Exhibits.
_________________

     Exhibits required to be filed with this Registration
Statement are listed in the following Exhibit Index.  Certain of
such exhibits that previously have been filed with the Securities
and Exchange Commission and that are designated by reference to
prior filings are incorporated by reference and made a part of
this Registration Statement.

Item 9.  Undertakings.
_____________________

     (a)  The undersigned registrant hereby undertakes:

          (1)  To file, during any period in which offers or
     sales are being made, a post-effective amendment to this
     registration statement:

               (i)  To include any prospectus required by section
          10(a)(3) of the Securities Act of 1933;

               (ii) To reflect in the prospectus any facts or
          events arising after the effective date of the
          registration statement (or the most recent post-
          effective amendment thereof) which, individually or in
          the aggregate, represent a fundamental change in the
          information in the registration statement. To reflect
          in the prospectus any facts or events arising after the
          effective date of the registration statement (or the
          most recent post-effective amendment thereof) which,
          individually or in the aggregate, represent a
          fundamental change in the information set forth in the
          registration statement.  Notwithstanding the foregoing,
          any increase or decrease in volume of securities
          offered (if the total dollar value of securities
          offered would not exceed that which was registered) and
          any deviation from the low or high end of the estimated
          maximum offering range may be reflected in the form of
          prospectus filed with the Commission pursuant to Rule
          424 (b) (230.424(b) of this chapter) if, in the
          aggregate, the changes in volume and price represent no
          more than a 20 percent change in the maximum aggregate
          offering price set forth in the "Calculation of
          Registration Fee" table in the effective registration
          statement;

               (iii)     To include any material information with
          respect to the plan of distribution not previously
          disclosed in the registration statement or any material
          change to such information in the registration
          statement.

          (2)  That, for the purpose of determining any liability
     under the Securities Act of 1933, each such post-effective
     amendment shall be deemed to be a new registration statement
     relating to the securities offered therein, and the offering
     of such securities at that time shall be deemed to be the
     initial bona fide offering thereof.

          (3)  To remove from registration by means of a post-
     effective amendment any of the securities being registered
     which remain unsold at the termination of the offering.

     (b)  The undersigned registrant hereby undertakes that, for
purposes of determining any liability under the Securities Act of
1933, each filing of the registrant's annual report pursuant to
section 13(a) or section 15(d) of the Securities Exchange Act of
1934 (and, where applicable, each filing of an employee benefit
plan's annual report pursuant to section 15(d) of the Securities
Exchange Act of 1934) that is incorporated by reference in the
registration statement shall be deemed to be a new registration



statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be
the initial bona fide offering thereof.

     (c)  The undersigned registrant hereby undertakes that, for
purposes of determining any liability under the Securities Act of
1933, each filing of the registrant's annual report pursuant to
section 13(a) or section 15(d) of the Securities Exchange Act of
1934 (and, where applicable, each filing of an employee benefit
plan's annual report pursuant to section 15(d) of the Securities
Exchange Act of 1934) that is incorporated by reference in the
registration statement shall be deemed to be a new registration
statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be
the initial bona fide offering thereof.

     (d)  Insofar as indemnification for liabilities arising
under the Securities Act of 1933 may be permitted to directors,
officers and controlling persons of the registrant pursuant to
the foregoing provisions, or otherwise, the registrant has been
advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as
expressed in the Act and is, therefore, unenforceable.  In the
event that a claim for indemnification against such liabilities
(other than the payment by the registrant of expenses incurred or
paid by a director, officer or controlling person of the
registrant in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling
person in connection with the securities being registered, the
registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of
appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in
the Act and will be governed by the final adjudication of such
issue.




                              SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933,
the registrant certifies that it has reasonable grounds to
believe that it meets all of the requirements for filing on Form
S-8 and has duly caused this Registration Statement to be signed
on its behalf by the undersigned, thereunto duly authorized, in
the City of Jacksonville, State of Florida, on February 1, 2006.

                            PATRIOT TRANSPORTATION HOLDING, INC.
                                (Registrant)

                            By:/s/ John E. Anderson
			       _________________________________
                                Name: John E. Anderson
                                Title:   President and Chief
		                         Executive Officer


                           POWER OF ATTORNEY
			   _________________

     Each of the undersigned officers and directors of Patriot
Transportation Holding, Inc., a Florida corporation, hereby
constitutes and appoints John E. Anderson and Ray M. Van
Landingham and each of them, severally, as his or her attorney-in-
fact and agent, with full power of substitution and
resubstitution, in his or her name and on his or her behalf, to
sign in any and all capacities this Registration Statement and
any and all amendments (including post-effective amendments) and
exhibits to this Registration Statement and any and all
applications and other documents relating thereto, with the
Securities and Exchange Commission, with full power and authority
to perform and do any and all acts and things whatsoever which
any such attorney or substitute may deem necessary or advisable
to be performed or done in connection with any or all of the
above-described matters, as fully as each of the undersigned
could do if personally present and acting, hereby ratifying and
approving all acts of any such attorney or substitute.

     Pursuant to the requirements of the Securities Act of 1933,
this registration statement has been signed by the following
persons in the capacities and on the date indicated.



Signature           Title             Signature         Title


/s/ John E. Anderson		      /s/ Luke E. Fichthorn III
_____________________________	      ___________________________
John E. Anderson, President           Luke E. Fichthorn III, Director
and Chief Executive Officer           Date:  February 1, 2006
(Principal Executive Officer)
and Director
Date: February 1, 2006






/s/ Edward L. Baker 		      /s/ John D. Klopfenstein
_____________________________	      ___________________________
Edward L. Baker, Director             John D. Klopfenstein, Controller
Date: February 1, 2006                and Chief Accounting Officer
                                      (Principal Accounting
                                      Officer)
                                      Date: February 1, 2006


/s/ John D. Baker II		      /s/ Robert H. Paul
_____________________________         ___________________________
John D. Baker II, Director            Robert H. Paul III, Director
Date: February 1, 2006                Date: February 1, 2006



/s/ Thompson S. Baker II	     /s/ H. W. Shad III
_____________________________	     ____________________________
Thompson S. Baker II, Director       H. W. Shad III, Director
Date: February 1, 2006               Date: February 1, 2006



/s/ Charles E. Commander III	     /s/ Martin E. Stein, Jr.
_____________________________	     ____________________________
Charles E. Commander III, Director   Martin E. Stein, Jr., Director
Date: February 1, 2006               Date: February 1, 2006



/s/ Ray M. Van Landingham	     /s/ James H. Winston
_____________________________	     ____________________________
Ray M. Van Landingham, Vice          James H. Winston, Director
President, Treasurer, Secretary      Date: February 1, 2006
and Chief Financial
Officer (Principal Financial Officer)
Date: February 1, 2006


     Pursuant to the requirements of the Securities Act of 1933,
the Chairman of the Compensation Committee (which administers the
Plan) has duly caused this Registration Statement to be signed on
its behalf by the undersigned, thereunto duly authorized, in the
City of Jacksonville, State of Florida on February 1, 2006.


                         The   Patriot  Transportation   Holding,
                         Inc. 2006 Stock Incentive Plan


                         By:  /s/ Robert H. Paul III
                            __________________________________
                              Name: Robert H. Paul III
                              Title: Chairman, Compensation
				     Committee





                	  Index to Exhibits

       
No.	  Description


(3)(a)(1) Articles of Incorporation of Patriot Transportation
          Holding, Inc., incorporated by reference to the
          corresponding exhibit filed with Form S-4 dated
          December 13, 1988.  File No. 33-26115.

(3)(a)(2) Amendment to the Articles of Incorporation of Patriot
          Transportation Holding, Inc., filed with the Secretary
          of State of Florida on February 19, 1991 incorporated
          by reference to the corresponding exhibit filed with
          Form 10-K for the fiscal year ended September 30, 1993.
          File No. 33-26115.

(3)(a)(3) Amendment to the Articles of Incorporation of Patriot
          Transportation Holding, Inc., filed with the Secretary
          of State of State of Florida on February 7, 1995,
          incorporated by reference to an appendix to the
          Company's Proxy Statement dated December 15, 1994. File
          No. 33-26115.

 (3)(a)(5)Amendment to the Articles of Incorporation of
          Patriot Transportation Holding, Inc., filed with the
          Florida Secretary of State on May 6, 1999 incorporated
          by reference to a form of such amendment filed as
          Exhibit 4 to the Company's Form 8-K dated May 5, 1999.
          File No. 33-26115.

(3)(a)(6) Amendment to the Articles of Incorporation of Patriot
          Transportation Holding, Inc., filed with the Secretary
          of State of Florida on February 21, 2000, incorporated
          by reference to the corresponding exhibit filed with
          Form 10-Q for the quarter ended March 31, 2000. File
          No. 33-26115.

(3)(b)(1) Amended and Restated Bylaws of Patriot Transportation
          Holding, Inc., adopted August 3, 2005, incorporated by
          reference to Exhibit 3.1 to the Form 8-K dated August
          3, 2005.

(4)(a)    Articles III, VII and XII of the Articles of
          Incorporation of Patriot Transportation Holding, Inc.,
          incorporated by reference to an exhibit filed with Form
          S-4 dated December 13, 1998;  Amended Article III,
          incorporated by reference to an exhibit filed with Form
          10-K for the fiscal year ended September 30, 1993; and
          Articles XIII and XIV, incorporated by reference to an
          appendix filed with the Company's Proxy Statement dated
          December 15, 1994. File No. 33-26115.

(4)(b)    Specimen stock certificate of Patriot Transportation
          Holding, Inc., incorporated by reference to an exhibit
          filed with Form S-4 dated December 13, 1988.

(4)(c)    Rights Agreement, dated as May 5, 1999 between the
          Company and First Union National Bank, incorporated by
          reference to Exhibit 4 of the Company's Form 8-K dated
          May 5, 1999. File No. 33-26115.

5.1       Opinion of Counsel.

23.1      Consent of PricewaterhouseCoopers LLP.