UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-Q/A

(Amendment No. 1)

QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF

THE SECURITIES EXCHANGE ACT OF 1934

For the Quarterly Period Ended June 30, 2008

Commission File Number : 001-32587

PHARMATHENE, INC.

(Exact name of registrant as specified in its charter)

Delaware		20-2726770
(State or other jurisdiction of		(I.R.S. Employer
incorporation or organization)		Identification No.)

One Park Place, Suite 450, Annapolis, MD 21401

(Address of principal executive offices)

Registrant’s telephone number, including area code: (410) 269-2600

Indicate by check whether the registrant (1) filed all reports required to be filed by Section 13 or 15(d) of the Exchange Act of 1934 during the past 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 o

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 the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one)

o Large accelerated filer	o Accelerated filer
o Non-accelerated filer	x Smaller reporting company

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

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date:

The number of shares of the registrant’s Common Stock, par value $0.0001 per share, outstanding as of August 13, 2008 was 22,087,121.

EXPLANATORY NOTE

On August 14, 2008, PharmAthene, Inc. (the “Company”) filed its quarterly report on Form 10-Q for the period ended June 30, 2008 (the “Original 10-Q”). This Amendment No. 1 to Form 10-Q (“Amendment No. 1”) is being filed to include as exhibits certain material agreements with respect to which the Company is requesting confidential treatment.

In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by the Company’s principal executive officer and principal financial officer are being filed or furnished as exhibits to this Amendment No. 1.

This Amendment No. 1 should be read in conjunction with the Original 10-Q, which continues to speak as of the date thereof. Except as specifically noted above, this Amendment No. 1 does not modify or update any other item or disclosure in the Original 10-Q. Accordingly, this Amendment No. 1 does not reflect events occurring after the filing of the Original 10-Q or modify, amend or update any related or other disclosures.

PART II

Item 6. Exhibits.

No.		Description

2.1		Amendment Agreement, dated April 2, 2008, among Avecia Investments Limited and Others and PharmAthene, Inc. and Others relating to a Sale and Purchase Agreement entered into on March 20, 2008 in respect of the Avecia Vaccines Business (incorporated by reference to Exhibit 2.1 to PharmAthene’s Current Report on Form 8-K filed on April 8, 2008).

3.1		Amended and Restated Certificate of Incorporation of PharmAthene, Inc., as amended on June 13, 2008 (incorporated by reference to Exhibit 3.1 to PharmAthene Inc.’s Current Report on Form 8-K filed on June 19, 2008).

3.2		Bylaws of PharmAthene, Inc., as amended on April 28, 2008 (incorporated by reference to Exhibit 3.1 to PharmAthene, Inc’s Current Report on Form 8-K filed on May 2, 2008).

10.29		Transitional Services Agreement, dated April 2, 2008, between Avecia Biologics Limited and PharmAthene UK Limited (incorporated by reference to Exhibit 10.29 to PharmAthene’s Current Report on Form 8-K/A filed on June 18, 2008).

10.30		Form of PharmAthene Inc. Executive Employment Agreement.*

10.31		Form of PharmAthene Inc. Confidentiality and Non-Disclosure Agreement.*

10.32		Master Services Agreement, dated April 2, 2008, between PharmAthene UK Limited and Avecia Biologics Limited.*, +

10.33		Master Service Agreement, dated December 15, 2004, between Avecia Limited and the Secretary of State for Defence, acting through the Defence Science and Technology Laboratory (DSTL) +

10.34		Master Service Agreement, dated August 18, 2005, between Avecia Limited and DSTL +

10.35		Manufacturing Licence Agreement, dated June 20, 2006, between Avecia Limited and DSTL +

10.36		Manufacturing and Marketing Licence Agreement, dated December 4, 2006, between Avecia Limited and DSTL +

10.37		Letter Agreement, dated March 20, 2008, between Avecia Biologics Limited and DSTL, relating to the Manufacturing Licence Agreement and the Manufacturing and Marketing Licence Agreement +

10.38		PharmAthene, Inc. 2007 Long-Term Incentive Compensation Plan, as amended on April 13, 2008 (incorporated by reference to Annex B to PharmAthene Inc.’s Definitive Proxy Statement on Schedule 14A filed on May 15, 2008).

31.1		Certification of Principal Executive Officer Pursuant to SEC Rule 13a-14(a)/15d-14(a).

31.2		Certification of Principal Financial Officer Pursuant to SEC Rule 13a-14(a)/15d-14(a).

32.1		Certification of Principal Executive Officer Pursuant to 18 U.S.C. Section 1350.

32.2		Certification of Principal Financial Officer Pursuant to 18 U.S.C. Section 1350.

* Previously filed.

+ Portions of this exhibit have been omitted pursuant to a request for confidential treatment.

SIGNATURES

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

	PHARMATHENE, INC.


Dated: August 19, 2008	By:	/s/ David P. Wright
		David P. Wright
		Chief Executive Officer


Dated: August 19, 2008	By:	/s/ Christopher C. Camut
		Christopher C. Camut
		Chief Financial Officer