SecProbe.io

Mail Stop 4720       September 17, 2009
Via Facsimile and U.S. Mail

David P. Wright Chief Executive Officer PharmAthene, Inc. One Park Place, Suite 450 Annapolis, Maryland 21401
 Re: PharmAthene, Inc.
  Amendment No. 1 to Registra tion Statement on Form S-3
  Filed August 31, 2009
  File No. 333-161587

Dear Mr. Wright:
This is to advise you that we  have limited our review of the above information statement
to the issues identified below.  We will make no further review of this filing.
Where indicated, we think you should revise  your document in response to these
comments.  If you disagree, we will consider your explanation as to why our comment is
inapplicable or a revision is unnecessary.  Please be as detailed as necess ary in your explanation.
After reviewing this information, we ma y or may not raise additional comments.
 Please understand that the purpose of our re view process is to assist you in your
compliance with the applicable disclosure requir ements and to enhance the overall disclosure in
your filing. We look forward to working with you in these respects. We welcome any questions
you may have about our comments or on any other as pect of our review. Feel free to call us at
the telephone numbers listed at the end of this letter.
 General

1. We note that you are registering the sale of 11,704,010 common shares. Given the size relative to the number of shares outstan ding held by non-affiliates, the nature of
the offering and the selling security holders , the transaction app ears to be a primary
offering. Because you are not eligible to conduct a primary offering on Form S-3 you
are not eligible to conduct a primary at-t he-market offering under Rule 415(a)(4).

David P. Wright
PharmAthene, Inc. September 17, 2009
Page 2
If you disagree with our analysis, please a dvise the staff of the company’s basis for
determining that the transaction is appropriately characterized as a transaction that is eligible to be made under Rule 415(a)(1)(i) .  In your analysis, please address the
following among any other relevant factors:

• The date on which and the manner in which each selling shareholder received the shares and/or the overlying securities;

• The relationship of each selling shareholder with the company, including an
analysis of whether the selling sharehol der is an affiliate of the company;

• Any relationships among th e selling shareholders;

• The dollar value of the shares registered in relation to the proceeds that the company received from the selling share holders for the securities, excluding
amounts of proceeds that were returned (or will be returned) to the selling
shareholders and/or their affiliates in fees or other payments;

• The discount at which the shareholders will purchase the common stock underlying the convertible notes (or any re lated security, such as a warrant or
option) upon conversion or exercise; and

• Whether or not any of the selling shareholders is in the business of buying and selling securities.

2. Please provide us, with a view toward disc losure in the prospectus, with the total
dollar value of the securitie s underlying the c onvertible notes and warrants that you
have registered for resale (using the number of underl ying securities that you have
registered for resale and the market price per share for those secu rities on the date of
the sale of the convertib le notes and warrants).

3. Please provide us, with a view toward disc losure in the prospectus, with tabular
disclosure of the dollar amount of each paym ent (including the value of any payments
to be made in common stock) in connecti on with the transaction that you have made
or may be required to make to any selling shareholder, any affiliate of a selling shareholder, or any person with whom any selling shareholder has a contractual relationship regarding the tr ansaction (including any interest payments, liquidated
damages, payments made to “finders” or “placement agents,” and any other payments or potential payments).  Please provide foot note disclosure of the terms of each such
payment.  Please do not include any repaymen t of principal on the convertible notes
in this disclosure.

Further, please provide us, with a view to ward disclosure in the prospectus, with
disclosure of the net proceeds to the issuer from the sale of the convertible notes and

David P. Wright
PharmAthene, Inc. September 17, 2009
Page 3
warrants and the total possible payments to all selling shareholders and any of their
affiliates in the first year following the sale of convertible notes.

4. Please provide us, with a view toward disc losure in the prospectus, with tabular
disclosure of:

• the total possible profit the selling share holders could realize as a result of the
conversion discount for the securitie s underlying the convertible notes,
presented in a table with the following  information disclosed separately:

o the market price per share of  the securities underlying the
convertible notes on the date of the sale of the convertible notes;

o the conversion price per share of  the underlying securities on the
date of the sale of the convertible notes, calculated as follows:

ƒ if the conversion price per share is set at a fixed price, use
the price per share established in the convertible notes; and

ƒ if the conversion price per shar e is not set at a fixed price
and, instead, is set at a floating rate in relationship to the market price of the underlying security, use the conversion
discount rate and the market ra te per share on the date of
the sale of the convertible  notes and determine the
conversion price per share as of that date;

• the total possible shares underlying the c onvertible notes (assuming no interest
payments and complete conversion th roughout the term of the notes);

• the combined market price of the total number of shares underlying the
convertible notes, calculated by using the market price per share on the date of
the sale of the convertible notes and the total possible shares underlying the
convertible notes;

• the total possible shares the selling shareholders may receive and the
combined conversion price of the to tal number of shares underlying the
convertible notes calculated  by using the conversion price on the date of the
sale of the convertible no tes and the total possible num ber of shares the selling
shareholders may receive; and

• the total possible discount to  the market price as of th e date of the sale of the
convertible notes, calculated by subtr acting the total conversion price on the
date of the sale of the convertible note s from the combined market price of the
total number of shares underlying th e convertible notes on that date.

David P. Wright
PharmAthene, Inc. September 17, 2009
Page 4
If there are provisions in th e convertible notes that coul d result in a change in the
price per share upon the occurrence of cer tain events, please provide additional
tabular disclosure as appropriate.  For exam ple, if the conversion price per share is
fixed unless and until the market price falls below a stated price, at which point the
conversion price per share drops to a lower price, please provide additional
disclosure.

5. Please provide us, with a view toward disclosure in the prospectus, with tabular
disclosure of:

• the total possible profit to be realized as a result of  any conversion discounts
for securities underlying any other warrants, options, notes, or other securities of the issuer that are held by the selling shareholders or any affiliates of the selling shareholders, presented in a table with the following information
disclosed separately:

o market price per share of the unde rlying securities on the date of
the sale of that other security;

o the conversion/exercise price per shar e as of the date of the sale of
that other security, cal culated as follows:

ƒ if the conversion/exercise pric e per share is set at a fixed
price, use the price per share on the date of the sale of that
other security; and

ƒ if the conversion/exercise pric e per share is not set at a
fixed price and, instead, is set at a floating rate in
relationship to the market pr ice of the underlying security,
use the conversion/exercise di scount rate and the market
rate per share on the date of th e sale of that other security
and determine the conversion price per share as of that date;

• the total possible shares  to be received under the particular securities
(assuming complete conversion/exercise);

• the combined market price of th e total number of underlying shares,
calculated by using the market price per sh are on the date of the sale of that
other security and the total possible shares to be received;

• the total possible shares to  be received and the comb ined conversion price of
the total number of shares underlying th at other security calculated by using
the conversion price on the date  of the sale of that ot her security and the total
possible number of underlying shares; and

David P. Wright
PharmAthene, Inc. September 17, 2009
Page 5
• the total possible discount to the market price as of the date of the sale of that
other security, calculated by subtracting the total conversion/exercise price on
the date of the sale of that other secu rity from the combined market price of
the total number of underly ing shares on that date.

6. Please provide us, with a view toward disclosure in the prospectus, with tabular
disclosure of:

• the gross proceeds paid or payable to  the issuer in the convertible note
transaction;

• all payments that have been made or that may be required to be made by the
issuer that are disclosed in response to Comment 3 above;

• the resulting net proceeds to the issuer; and

• the combined total possible profit to be realized as a result of any conversion
discounts regarding the secu rities underlying the c onvertible notes and any
other warrants, options, notes, or other s ecurities of the issuer that are held by
the selling shareholders or any affiliates of the sell ing shareholders that is
disclosed in response to Comm ent 4 and Comment 5 above.

Further, please provide us, with a view to ward disclosure in the prospectus, with
disclosure – as a percentage – of the total amount of all possible payments as
disclosed in response to Comment 3 and th e total possible discount to the market
price of the shares underlyi ng the convertible note as disclosed in response to
Comment 4 divided by the net proceeds to the issuer from the sale of the convertible
notes, as well as the amount of that resulting percentage averaged over the term of the
convertible notes.

7. Please provide us, with a view toward disclosure in the prospectus, with tabular
disclosure of all prior securities transact ions between the issuer (or any of its
predecessors) and the selling shareholders, any affiliates of the selling shareholders,
or any person with whom any selling shareholder has a contractual relationship regarding the transaction (or any predecesso rs of those persons), with the table
including the following information disclo sed separately for each transaction:

• the date of the transaction;

• the number of shares of the class of secu rities subject to the transaction that
were outstanding prior to the transaction;

• the number of shares of the class of secu rities subject to the transaction that
were outstanding prior to the transacti on and held by persons other than the

David P. Wright
PharmAthene, Inc. September 17, 2009
Page 6
selling shareholders, affiliates of th e company, or affiliates of the selling
shareholders;

• the number of shares of the class of secu rities subject to the transaction that
were issued or issuable in connection with the transaction;

• the percentage of total is sued and outstanding securiti es that were issued or
issuable in the transaction (assuming full issuance), with the percentage
calculated by taking the number of shar es issued and outstanding prior to the
applicable transaction and held by persons other than the selling shareholders,
affiliates of the company, or affiliates of the selling shareholders, and dividing
that number by the number of shares issued  or issuable in connection with the
applicable transaction;

• the market price per share of the class of  securities subject to the transaction
immediately prior to the tran saction (reverse split adju sted, if necessary); and

• the current market price per share of the class of securities subject to the
transaction (reverse split adjusted, if necessary).

8. Please provide us, with a view toward disclosure in the prospectus, with tabular
disclosure comparing:

• the number of shares outstanding prior to the convertible note transaction that
are held by persons other than the se lling shareholders, affiliates of the
company, and affiliates of the selling shareholders;

• the number of shares registered for re sale by the selling shareholders or
affiliates of the selling shareholders in prior registration statements;

• the number of shares registered for re sale by the selling shareholders or
affiliates of the selling shareholders that continue to be held by the selling
shareholders or affiliates of the selling shareholders;

• the number of shares that have been sold in registered resa le transactions by
the selling shareholders or affiliates of the selling shareholders; and

• the number of shares registered for resale  on behalf of the selling shareholders
or affiliates of the selling sharehol ders in the current transaction.
 In this analysis, the calculation of the number of outstanding shares should not
include any securities underl ying any outstanding convertib le securities, options, or
warrants.

David P. Wright
PharmAthene, Inc. September 17, 2009
Page 7
9. Please provide us, with a view toward disclosure in the prospectus , with the following
information:

• whether the issuer has the intention, and a reasonable basis to believe that it
will have the financial ability, to make all payments on the overlying securities; and

• whether – based on information obtained from the selling shareholders – any
of the selling shareholders have an existing short position in the company’s
common stock and, if any of the selling shareholders have an existing short
position in the company’s stock, the following additional information:

o the date on which each such selli ng shareholder entered into that
short position; and
 o the relationship of the date on which each such selling shareholder entered into that short position to the date of th e announcement of
the convertible note transaction a nd the filing of the registration
statement ( e.g., before or after the announ cement of the convertible
note transaction, before the fili ng or after the filing of the
registration statement, etc.).

10. Please provide us, with a view toward disclosure in the prospectus, with:

• a materially complete description of the relationships and arrangements that
have existed in the past three years or  are to be performed in the future
between the issuer (or any of its predecessors) and the selling shareholders,
any affiliates of the selling shareholders , or any person with whom any selling
shareholder has a contractual relationsh ip regarding the transaction (or any
predecessors of those persons) – the in formation provided should include, in
reasonable detail, a complete descripti on of the rights and obligations of the
parties in connection with the sale of the convertible notes; and

• copies of all agreements between the issuer (or any of its predecessors) and
the selling shareholders, any affiliates of the selling shareholders, or any person with whom any selling share holder has a contractual relationship
regarding the transaction (or any predece ssors of those persons) in connection
with the sale of the convertible notes.

If it is your view th at such a description of the relationships and arrangements
between and among those parties already