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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2013-06-28</periodOfReport>

    <notSubjectToSection16>false</notSubjectToSection16>

    <issuer>
        <issuerCik>0000911326</issuerCik>
        <issuerName>SYNAGEVA BIOPHARMA CORP</issuerName>
        <issuerTradingSymbol>GEVA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001532219</rptOwnerCik>
            <rptOwnerName>Quinn Anthony</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>33 HAYDEN AVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>LEXINGTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02421</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>false</isDirector>
            <isOfficer>true</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
            <officerTitle>SVP, Chief Medical Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <transactionDate>
                <value>2013-06-28</value>
                <footnoteId id="F2"/>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>5</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>297</value>
                    <footnoteId id="F3"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>35.68</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>15332</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The reporting person is voluntarily reporting the acquisition of shares of the issuer's common stock pursuant to the Synageva BioPharma Corp. Employee Stock Purchase Plan (&quot;ESPP&quot;), for the ESPP purchase period of January 1, 2013 through June 30, 2013. This transaction is also exempt under Rule 16b-3(c).</footnote>
        <footnote id="F2">The Option Period (as defined in the ESPP) ended on June 30, 2013, so the shares were acquired on June 28, 2013, the last trading day prior to the end of the Option Period.</footnote>
        <footnote id="F3">In accordance with the ESPP, these shares were purchased based on 85% of the closing price of the issuer's common stock on June 28, 2013.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Anthony Quinn</signatureName>
        <signatureDate>2013-07-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
