<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-06-29</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000880431</issuerCik>
        <issuerName>GENAERA CORP</issuerName>
        <issuerTradingSymbol>GENR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001347039</rptOwnerCik>
            <rptOwnerName>Xmark Opportunity Partners, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>90 GROVE STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 201</rptOwnerStreet2>
            <rptOwnerCity>RIDGEFIELD</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06877</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 $0.002</value>
            </securityTitle>
            <transactionDate>
                <value>2009-06-29</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>42571</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.1015</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2795781</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">As of June 29, 2009, Xmark Opportunity Fund, L.P., a Delaware limited partnership (&quot;Opportunity LP&quot;), held 465,150 common shares, $0.002 par value per share (the &quot;Common Shares&quot;), of Genaera Corporation, a Delaware corporation (the &quot;Company&quot;).</footnote>
        <footnote id="F2">As of June 29, 2009, Xmark Opportunity Fund, Ltd., a Cayman Islands exempted company (&quot;Opportunity Ltd&quot;), held 1,181,923 Common Shares of the Company.  As of June 29, 2009, Xmark JV Investment Partners, LLC, a Delaware limited liability company (&quot;JV Partners&quot;), held 1,148,708 Common Shares of the Company.</footnote>
        <footnote id="F3">The reporting person, Xmark Opportunity Partners, LLC, a Delaware limited liability company (&quot;Opportunity Partners&quot;), is the sole member of the investment manager of Opportunity LP and Opportunity Ltd, and the investment manager of JV Partners, and, as such, possesses sole power to vote and direct the disposition of all securities of the Company held by Opportunity LP, Opportunity Ltd and JV Partners.  Opportunity Partners' interest in the securities reported herein is limited to the extent of its pecuniary interest in Opportunity LP, Opportunity Ltd and JV Partners, if any.  Mitchell D. Kaye and David C. Cavalier, the Co-Managing Members of Xmark Capital Partners, LLC, the Managing Member of Opportunity Partners, share voting and investment power with respect to all securities beneficially owned by Opportunity Partners.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>XMARK OPPORTUNITY PARTNERS, LLC, By: Xmark Capital Partners, LLC, its Managing Member, By: David C. Cavalier, Co-Managing Member, /s/ David C. Cavalier</signatureName>
        <signatureDate>2009-07-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
