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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 EHmuqlqcK1eoukRfWQu4O0M6z775iMxOjdqGhyanDm4ynDQWR61L3pwIti2Mbr6a
 8thGRHENaEJiYE2suzZ0VQ==

<SEC-DOCUMENT>0001209191-04-034221.txt : 20040702
<SEC-HEADER>0001209191-04-034221.hdr.sgml : 20040702
<ACCEPTANCE-DATETIME>20040702115326
ACCESSION NUMBER:		0001209191-04-034221
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20040701
FILED AS OF DATE:		20040702

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			HYBRIDON INC
		CENTRAL INDEX KEY:			0000861838
		STANDARD INDUSTRIAL CLASSIFICATION:	BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
		IRS NUMBER:				043072298
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		345 VASSAR STREET
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02139
		BUSINESS PHONE:		6176795500

	MAIL ADDRESS:	
		STREET 1:		345 VASSAR STREET
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02139

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			WYNGAARDEN JAMES B
		CENTRAL INDEX KEY:			0001022940

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-31918
		FILM NUMBER:		04898123

	BUSINESS ADDRESS:	
		STREET 1:		C/O GENAERA CORP
		STREET 2:		5110 CAMPUS DR
		CITY:			PLYMOUTH MEETING
		STATE:			PA
		ZIP:			19462
		BUSINESS PHONE:		610 941 4020

	MAIL ADDRESS:	
		STREET 1:		C/O GENAERA CORP
		STREET 2:		5110 CAMPUS DRIVE
		CITY:			PLYMOUTH MEETING
		STATE:			PA
		ZIP:			19462
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-07-01</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000861838</issuerCik>
        <issuerName>HYBRIDON INC</issuerName>
        <issuerTradingSymbol>HBY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001022940</rptOwnerCik>
            <rptOwnerName>WYNGAARDEN JAMES B</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3504 STONEYBROOK DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>DURHAM</rptOwnerCity>
            <rptOwnerState>NC</rptOwnerState>
            <rptOwnerZipCode>27705</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Options</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.64</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-07-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>3750</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-07-01</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-07-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3750</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3750</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes></footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>James Wyngaarden</signatureName>
        <signatureDate>2004-07-01</signatureDate>
    </ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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