<SEC-DOCUMENT>0000899243-16-035242.txt : 20161209
<SEC-HEADER>0000899243-16-035242.hdr.sgml : 20161209
<ACCEPTANCE-DATETIME>20161209165436
ACCESSION NUMBER:		0000899243-16-035242
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20161207
FILED AS OF DATE:		20161209
DATE AS OF CHANGE:		20161209

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			PHARMATHENE, INC
		CENTRAL INDEX KEY:			0001326190
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				202726770
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		ONE PARK PLACE, SUITE 450
		CITY:			ANNAPOLIS
		STATE:			MD
		ZIP:			21401
		BUSINESS PHONE:		410 269 2600

	MAIL ADDRESS:	
		STREET 1:		ONE PARK PLACE, SUITE 450
		CITY:			ANNAPOLIS
		STATE:			MD
		ZIP:			21401

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	HEALTHCARE ACQUISITION CORP
		DATE OF NAME CHANGE:	20050505

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			FROHLICH PHIL
		CENTRAL INDEX KEY:			0001127429
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-32587
		FILM NUMBER:		162044621

	MAIL ADDRESS:	
		STREET 1:		1924 SOUTH IRICA SUITE 1120
		CITY:			TULSA
		STATE:			OK
		ZIP:			741046529

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			PRESCOTT GROUP CAPITAL MANAGEMENT, L.L.C.
		CENTRAL INDEX KEY:			0001166152
		STATE OF INCORPORATION:			OK
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-32587
		FILM NUMBER:		162044622

	BUSINESS ADDRESS:	
		STREET 1:		1924 SOUTH UTICA
		STREET 2:		SUITE 1120
		CITY:			TULSA
		STATE:			OK
		ZIP:			74104-6429
		BUSINESS PHONE:		918-747-3412

	MAIL ADDRESS:	
		STREET 1:		1924 SOUTH UTICA
		STREET 2:		SUITE 1120
		CITY:			TULSA
		STATE:			OK
		ZIP:			74104-6429

	FORMER NAME:	
		FORMER CONFORMED NAME:	PRESCOTT GROUP CAPITAL MANAGEMENT LLC
		DATE OF NAME CHANGE:	20020128
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-12-07</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001326190</issuerCik>
        <issuerName>PHARMATHENE, INC</issuerName>
        <issuerTradingSymbol>PIP</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001166152</rptOwnerCik>
            <rptOwnerName>PRESCOTT GROUP CAPITAL MANAGEMENT, L.L.C.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1924 SOUTH UTICA, SUITE 1120</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>TULSA</rptOwnerCity>
            <rptOwnerState>OK</rptOwnerState>
            <rptOwnerZipCode>74104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001127429</rptOwnerCik>
            <rptOwnerName>FROHLICH PHIL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1924 SOUTH UTICA, SUITE 1120</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>TULSA</rptOwnerCity>
            <rptOwnerState>OK</rptOwnerState>
            <rptOwnerZipCode>74014</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2016-12-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>477829</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.26</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7503206</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2016-12-08</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>440479</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.25</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7062727</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2016-12-09</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>436324</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.26</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>6626403</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The filing of this Form 4 shall not be construed as an admission that Prescott Group Capital Management, L.L.C. (&quot;Prescott Capital&quot;) or Phil Frohlich, the manager of Prescott Capital, is or was, for the purposes of Section 16(a) of the Securities Exchange Act of 1934, as amended, or otherwise, the beneficial owner of any of the shares of Common Stock, par value $0.0001 per share (the &quot;Common Stock&quot;), of PharmAthene, Inc. (the &quot;Issuer&quot;) purchased by Prescott Group Aggressive Small Cap Master Fund, G.P. (the &quot;Master Fund&quot;) for the accounts of Prescott Group Aggressive Small Cap, L.P. or Prescott Group Aggressive Small Cap II, L.P. (together, the &quot;Small Cap Funds&quot;).  Pursuant to Rule 16a-1, both Prescott Capital and Phil Frohlich disclaim such beneficial ownership.</footnote>
        <footnote id="F2">Prescott Capital holds indirectly the shares of Common Stock of the Issuer through the account of the Master Fund, of which Prescott Capital is the Investment Manager.  The Master Fund holds the shares of Common Stock for the accounts of the Small Cap Funds, of which Prescott Capital is the Investment Manager.  Prescott Capital receives a portion of the profits in the way of a capital allocation from, and owns a partnership interest in, the Small Cap Funds.  Phil Frohlich reports the Common Stock held indirectly by  Prescott Capital because, as the manager of Prescott Capital at the time of purchase, he controlled the disposition and voting of the securities.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Phil Frohlich, manager of Prescott Group Capital Management, L.L.C.</signatureName>
        <signatureDate>2016-12-09</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Phil Frohlich</signatureName>
        <signatureDate>2016-12-09</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
