Exhibit 5.1

		1221 Avenue of the Americas
		New York, NY 10020
		212.768.6700
		212.768.6800 fax
		www.sonnenschein.com
	November 19, 2009

PharmAthene, Inc.

One Park Place

Suite #450

Annapolis, MD 21401

Re:   Amendment No. 2 to Registration Statement on Form S-3

Ladies and Gentlemen:

In our capacity as counsel to PharmAthene, Inc., a Delaware corporation (the “Company”), we have been asked to render this opinion in connection with amendment no. 2 to the registration statement on Form S-3 (File No. 333-161587) (as so amended, the “Registration Statement”), being filed contemporaneously herewith by the Company with the Securities and Exchange Commission (the “Commission”) under the Securities Act of 1933, as amended (the “Act”), covering 4,582,659 shares (the “Note Shares”) of common stock, par value $0.0001 per share, of the Company (the “Common Stock”) representing a portion of the up to 9,131,235 shares of Common Stock that are issuable upon the conversion of certain 10% convertible notes heretofore issued by the Company (the “Notes”), assuming conversion of all Notes on the maturity date thereof.  The Note Shares have been included in the Registration Statement for the account of the persons identified therein as the Selling Stockholders.

We are delivering this opinion to you at your request in accordance with the requirements of Item 601(b)(5) of Regulation S-K under the Act.

In connection with rendering this opinion, we have examined and are familiar with (i) the Company’s Amended and Restated Certificate of Incorporation, as amended, (ii) the Company’s By-Laws, (iii) the Registration Statement, (iv) corporate proceedings of the Company relating to the Notes and the Note Shares, and (v) such other instruments and documents as we have deemed relevant under the circumstances.

In making the aforesaid examinations, we have assumed the genuineness of all signatures and the conformity to original documents of all copies furnished to us as original or photostatic copies. We have also assumed that the corporate records furnished to us by the Company include all corporate proceedings taken by the Company to date.

Based upon the foregoing and subject to the assumptions and qualifications set forth herein, we are of the opinion that the Note Shares have been duly and validly authorized and, when issued in accordance with the terms of the Notes, will be duly and validly issued, fully paid and non-assessable.

The foregoing opinion is limited to the laws of the United States of America and Delaware corporate law (which includes the Delaware General Corporation Law and applicable provisions of the Delaware constitution, as well as reported judicial opinions interpreting same), and we do not purport to express any opinion on the laws of any other jurisdiction.

We hereby consent to the use of our opinion as an exhibit to the Registration Statement and to the reference to this firm and this opinion under the heading “Legal Matters” in the prospectus comprising a

Brussels  Chicago  Dallas  Kansas City  Los Angeles  New York  Phoenix  St. Louis
San Francisco  Short Hills, N.J.  Silicon Valley  Washington, D.C.  Zurich

PharmAthene, Inc.

November 19, 2009

Page 2

part of the Registration Statement and any amendment thereto.  In giving such consent, we do not hereby admit that we come within the category of persons whose consent is required under Section 7 of the Act, or the rules and regulations of the Commission thereunder.

Very truly yours,

/s/ Sonnenschein Nath & Rosenthal LLP

SONNENSCHEIN NATH & ROSENTHAL LLP

2