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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2017-12-19</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001053650</issuerCik>
        <issuerName>OMEGA PROTEIN CORP</issuerName>
        <issuerTradingSymbol>OME</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001029703</rptOwnerCik>
            <rptOwnerName>HELD JOHN D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>2105 CITY WEST BOULEVARD, SUITE 500</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>HOUSTON</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>77042</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2017-12-19</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>68472</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>22.00</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Includes shares of common stock (the &quot;Common Stock&quot;) of Omega Protein Corporation (the &quot;Company&quot;) held by the Reporting Person and awards of shares of restricted Common Stock previously granted, 13,244 shares of which vested immediately prior to the effective time of the Merger (as defined below).</footnote>
        <footnote id="F2">On December 19, 2017, pursuant to the Agreement and Plan of Merger dated as of October 5, 2017 (the &quot;Merger Agreement&quot;), by and among the Company, Cooke Inc. (&quot;Cooke&quot;) and Alpha MergerSub, Inc. (&quot;Merger Sub&quot;), Merger Sub merged with and into the Company (the &quot;Merger&quot;) with the Company continuing as the surviving entity and a wholly-owned indirect subsidiary of Cooke. Pursuant to the Merger Agreement, each share of Common Stock of the Company issued and outstanding immediately prior to the effective time of the merger was automatically cancelled and converted into the right to the receive $22.00 in cash, less any required tax withholdings.</footnote>
    </footnotes>

    <remarks>Executive VP, General Counsel &amp; Secretary</remarks>

    <ownerSignature>
        <signatureName>/s/ John D. Held</signatureName>
        <signatureDate>2017-12-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
