10-K/A

        UNITED STATES
	SECURITIES AND EXCHANGE COMMISSION
	Washington, D.C. 20549
	FORM 10-K/A
        (Amendment No.1)
(Mark One)
   [X]	 ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d)
	OF THE SECURITIES EXCHANGE ACT OF 1934
           For the fiscal year ended September 30, 2011
	OR
   [ ] 	TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
	OF THE SECURITIES EXCHANGE ACT OF 1934
	Commission file number 33-26115

	PATRIOT TRANSPORTATION HOLDING, INC.
	(Exact name of registrant as specified in its charter)

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

200 W. Forsyth Street, 7th Floor, Jacksonville, Florida		     32202
(Address of principal executive offices)			  (Zip Code)

Registrant's telephone number, including area code   904/396-5733

Securities registered pursuant to Section 12(b) of the Act:
Common Stock $.10 par value                     NASDAQ
     Title of class               Name of each exchange on which registered

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as
defined in Rule 405 of the Securities Act. Yes     No  X

Indicate by check mark if the registrant is not required to file reports
pursuant to Section 13 or 15(d) of the Act. Yes     No  X

Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act
of 1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to
such filing requirements for the past 90 days. Yes  X  No

Indicate by check mark whether the registrant has submitted electronically
and posted on its corporate Web site, if any, every Interactive Data File
required to be submitted and posted pursuant to Rule 405 of Regulation S-T
during the preceding 12 months (or for such shorter period that the
registrant was required to submit and post such files). Yes  X  No

Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained,
to the best of registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. [   ]

Indicate by check mark whether the registrant is a large accelerated filer,
an accelerated filer, a non-accelerated filer, or a smaller reporting
company.  See definitions of "large accelerated filer," "accelerated filer"
and "smaller reporting company" in Rule 12b-2 of the Exchange Act.

Large accelerated filer[ ]                  Accelerated filer[X]

Non-accelerated filer[ ]                    Smaller reporting company [ ]

Indicate by check mark whether the registrant is a shell company (as
defined in Rule 12b-2 of the Act). Yes         No   X

The number of shares of the registrant's stock outstanding as of November 30,
2011 was 9,283,610.  The aggregate market value of the shares of Common
Stock held by non-affiliates of the registrant as of March 31, 2011, the
last day of business of our most recently completed second fiscal quarter,
was $116,320,770.  Solely for purposes of this calculation, the registrant
has assumed that all directors, officers and ten percent (10%) shareholders
of the Company are affiliates of the registrant.

Documents Incorporated by Reference

Portions of the Patriot Transportation Holding, Inc. 2011 Annual Report to
Shareholders are incorporated by reference in Parts I and II.

Portions of the Patriot Transportation Holding, Inc. Proxy Statement which
was filed with the Securities and Exchange Commission on December 16, 2011
are incorporated by reference in Part III.



Explanatory Note

Patriot Transportation Holding, Inc. is filing this Amendment No. 1 to the
Company's Annual Report on Form 10-K for the fiscal year ended September
30, 2011, as originally filed on December 8, 2011, with the Securities and
Exchange Commission (referred to as the "Original Filing") to amend Part
III, Item 11, Item 13 and Item 14 of the Original Filing in order to
correct prior disclosure regarding sections incorporated by reference from
the Company's Proxy Statement.

No other changes have been made to the Form 10-K.  This Amendment No. 1 to
the Form 10-K speaks as of the original filing date of the Form 10-K, does
not reflect events that may have occurred subsequent to the original
filing date, and does not modify or update in any way disclosures made in
the original Form 10-K.






                          PART III

Item 11.  EXECUTIVE COMPENSATION.

Information required in response to this Item 11 is included
under the captions "Compensation Discussion and Analysis,"
"Executive Compensation," "Compensation Committee Report," "Non-
Employee Director Compensation," "Board Leadership Structure and
Committee Membership - Compensation Committee," and "Shareholder
Return Performance" in the Company's Proxy Statement and such
information is incorporated herein by reference.  The Proxy
Statement was filed with the Securities and Exchange Commission
on December 16, 2011.

Item 13.  CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS.

Information required in response to this Item 13 is included
under the caption "Related Party Transactions", "Corporate
Governance", and "Board Leadership Structure and Committee
Membership" in the Company's Proxy Statement and such
information is incorporated herein by reference. The Proxy
Statement was filed with the Securities and Exchange Commission
on December 16, 2011.

Item 14. PRINCIPAL ACCOUNTING FEES AND SERVICES.

Information required in response to this Item 14 is included
under the captions "Independent Registered Public Accounting
Firm" in the Company's Proxy Statement and such information is
incorporated herein by reference. The Proxy Statement was filed
with the Securities and Exchange Commission on December 16,
2011.










SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange
Act of 1934, the registrant has duly caused this report to be signed on its
behalf by the undersigned, thereunto duly authorized.

                                 Patriot Transportation Holding, Inc.


Date:  July 23, 2012         By THOMPSON S. BAKER II
                                Thompson S. Baker II
                                President and Chief Executive
                                Officer (Principal Executive Officer)



                             By JOHN D. MILTON, JR._____________
                                John D. Milton, Jr.
                                Executive Vice President, Treasurer,
                                Secretary and Chief Financial Officer
                                (Principal Financial Officer)


                             By JOHN D. KLOPFENSTEIN____________
                                John D. Klopfenstein
                                Controller and Chief Accounting
                                Officer(Principal Accounting Officer)




PATRIOT TRANSPORTATION HOLDING, INC.
FORM 10-K/A FOR THE FISCAL YEAR ENDED SEPTEMBER 30, 2011
EXHIBIT INDEX

(31)(a)           Certification of Thompson S. Baker II.
(31)(b)           Certification of John D. Milton, Jr..
(31)(c)           Certification of John D. Klopfenstein.

(32)			Certification of Chief Executive Officer, Chief
Financial Officer, and Chief Accounting Officer under Section 906 of the
Sarbanes-Oxley Act of 2002.

EX-31

CERTIFICATIONS                                                  Exhibit 31(c)

I, John D. Klopfenstein, certify that:

1.	I have reviewed this annual report on Form 10-K/A of Patriot
Transportation Holding, Inc.;
2.	Based on my knowledge, this annual report does not contain any untrue
statement of a material fact or omit to state a material fact necessary to
make the statements made, in light of the circumstances under which such
statements were made, not misleading with respect to the period covered by
this annual report;
3.	Based on my knowledge, the financial statements, and other financial
information included in this annual report, fairly present in all material
respects the financial condition, results of operations and cash flows of the
registrant as of, and for, the periods presented in this annual report;
4.	The registrant's other certifying officers and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined
in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over
financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-
15(f)) for the registrant and have:
a)	designed such disclosure controls and procedures, or caused such
disclosure controls to be designed under our supervision, ensure that
material information relating to the registrant, including its
consolidated subsidiaries, is made known to us by others within those
entities, particularly during the period in which this report is being
prepared;
b)	designed such internal control over financial reporting, or caused such
internal control over financial reporting to be designed under our supervision,
to provide reasonable assurance regarding the reliability of financial
reporting and the preparation of financial statements for external purposes
in accordance with generally accepted accounting principles;
c)	evaluated the effectiveness of the registrant's disclosure controls and
procedures and presented in this report our conclusions about the effectiveness
of the disclosures controls and procedures, as of the end of the period covered
by this report based on such evaluation; and
d)	disclosed in this report any changes in the registrant's internal
control over financial reporting that occurred during the registrant's most
recent fiscal annual that has materially affected, or is reasonably likely to
materially affect, the registrant's internal control over financial report; and
5.	The registrant's other certifying officers and I have disclosed, based
on our most recent evaluation of internal control over financial reporting, to
the registrant's auditors and the audit committee of registrant's board of
directors (or persons performing the equivalent functions):
a)	all significant deficiencies in the design or operation of internal
control over financial reporting which are reasonably likely to adversely
affect the registrant's ability to record, process, summarize and report
financial information; and
b)	any fraud, whether or not material, that involves management or other
employees who have a significant role in the registrant's internal control over
financial reporting.

Date: July 23, 2012                           /s/John D. Klopfenstein
                                              Controller and Chief Accounting
                                                Officer

EX-31

CERTIFICATIONS                                                  Exhibit 31(b)

I, John D. Milton, Jr., certify that:

1.	I have reviewed this annual report on Form 10-K/A of Patriot
Transportation Holding, Inc.;
2.	Based on my knowledge, this annual report does not contain any untrue
statement of a material fact or omit to state a material fact necessary to
make the statements made, in light of the circumstances under which such
statements were made, not misleading with respect to the period covered by
this annual report;
3.	Based on my knowledge, the financial statements, and other financial
information included in this annual report, fairly present in all material
respects the financial condition, results of operations and cash flows of the
registrant as of, and for, the periods presented in this annual report;
4.	The registrant's other certifying officers and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined
in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over
financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-
15(f)) for the registrant and have:
a)	designed such disclosure controls and procedures, or caused such
disclosure controls to be designed under our supervision, ensure that
material information relating to the registrant, including its
consolidated subsidiaries, is made known to us by others within those
entities, particularly during the period in which this report is being
prepared;
b)	designed such internal control over financial reporting, or caused such
internal control over financial reporting to be designed under our supervision,
to provide reasonable assurance regarding the reliability of financial
reporting and the preparation of financial statements for external purposes
in accordance with generally accepted accounting principles;
c)	evaluated the effectiveness of the registrant's disclosure controls and
procedures and presented in this report our conclusions about the effectiveness
of the disclosures controls and procedures, as of the end of the period covered
by this report based on such evaluation; and
d)	disclosed in this report any changes in the registrant's internal
control over financial reporting that occurred during the registrant's most
recent fiscal annual that has materially affected, or is reasonably likely to
materially affect, the registrant's internal control over financial report; and
5.	The registrant's other certifying officers and I have disclosed, based
on our most recent evaluation of internal control over financial reporting, to
the registrant's auditors and the audit committee of registrant's board of
directors (or persons performing the equivalent functions):
a)	all significant deficiencies in the design or operation of internal
control over financial reporting which are reasonably likely to adversely
affect the registrant's ability to record, process, summarize and report
financial information; and
b)	any fraud, whether or not material, that involves management or other
employees who have a significant role in the registrant's internal control over
financial reporting.

Date: July 23, 2012                           /s/John D. Milton, Jr.
                                              Executive Vice President,
                                                Treasurer, Secretary and
                                                Chief Financial Officer

EX-31

CERTIFICATIONS                                                  Exhibit 31(a)

I, Thompson S. Baker II, certify that:

1.	I have reviewed this annual report on Form 10-K/A of Patriot
Transportation Holding, Inc.;
2.	Based on my knowledge, this annual report does not contain any untrue
statement of a material fact or omit to state a material fact necessary to
make the statements made, in light of the circumstances under which such
statements were made, not misleading with respect to the period covered by
this annual report;
3.	Based on my knowledge, the financial statements, and other financial
information included in this annual report, fairly present in all material
respects the financial condition, results of operations and cash flows of the
registrant as of, and for, the periods presented in this annual report;
4.	The registrant's other certifying officers and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined
in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over
financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-
15(f)) for the registrant and have:
a)	designed such disclosure controls and procedures, or caused such
disclosure controls to be designed under our supervision, ensure that
material information relating to the registrant, including its
consolidated subsidiaries, is made known to us by others within those
entities, particularly during the period in which this report is being
prepared;
b)	designed such internal control over financial reporting, or caused such
internal control over financial reporting to be designed under our supervision,
to provide reasonable assurance regarding the reliability of financial
reporting and the preparation of financial statements for external purposes
in accordance with generally accepted accounting principles;
c)	evaluated the effectiveness of the registrant's disclosure controls and
procedures and presented in this report our conclusions about the effectiveness
of the disclosures controls and procedures, as of the end of the period covered
by this report based on such evaluation; and
d)	disclosed in this report any changes in the registrant's internal
control over financial reporting that occurred during the registrant's most
recent fiscal annual that has materially affected, or is reasonably likely to
materially affect, the registrant's internal control over financial report; and
5.	The registrant's other certifying officers and I have disclosed, based
on our most recent evaluation of internal control over financial reporting, to
the registrant's auditors and the audit committee of registrant's board of
directors (or persons performing the equivalent functions):
a)	all significant deficiencies in the design or operation of internal
control over financial reporting which are reasonably likely to adversely
affect the registrant's ability to record, process, summarize and report
financial information; and
b)	any fraud, whether or not material, that involves management or other
employees who have a significant role in the registrant's internal control over
financial reporting.

Date: July 23, 2012                           /s/Thompson S. Baker II
                                              President and Chief Executive
                                                Officer

EX-32

                                                                     Exhibit 32




CERTIFICATION UNDER SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002


Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, each of the
undersigned certifies that this periodic report fully complies with the
requirements of Section 13(a) or 15(d) of the Securities Exchange Act of
1934 and that information contained in this periodic report fairly
presents, in all material respects, the financial condition and results
of operations of Patriot Transportation Holding, Inc.

                                        PATRIOT TRANSPORTATION HOLDING, INC.


July 23, 2012                           THOMPSON S. BAKER II

                                        Thompson S. Baker II
                                        President and Chief Executive
                                        Officer


                                        JOHN D. MILTON, JR.

                                        John D. Milton, Jr.
                                        Executive Vice President,
                                        Treasurer, Secretary and
                                        Chief Financial Officer


                                        JOHN D. KLOPFENSTEIN

                                        John D. Klopfenstein
                                        Controller and Chief
                                        Accounting Officer


A signed original of this written statement required by Section 906 has been
provided to Patriot Transportation Holding, Inc. and will be retained by
Patriot Transportation Holding, Inc. and furnished to the Securities and
Exchange Commission or its staff upon request.

The foregoing certification accompanies the issuer's Annual Report on Form
10-K and is not filed as provided in SEC Release Nos. 33-8212, 34-4751 and
IC-25967, dated June 30, 2003.