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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2014-06-30</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>EVP, CMO &amp; Head of R&amp;D</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <transactionDate>
                <value>2014-06-30</value>
                <footnoteId id="F2"/>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>71</value>
                    <footnoteId id="F3"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>54.89</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>25595</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 option period of January 1, 2014 through June 30, 2014 (the &quot;Option Period&quot;). This transaction is also exempt under Rule 16b-3(c).</footnote>
        <footnote id="F2">The transaction occurred on the last day 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 January 2, 2014, the first trading day of the Option Period.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Anthony Quinn</signatureName>
        <signatureDate>2014-07-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
