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

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2007-08-28</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001302707</issuerCik>
        <issuerName>Horizon Lines, Inc.</issuerName>
        <issuerTradingSymbol>HRZ</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001052297</rptOwnerCik>
            <rptOwnerName>MANDL ALEX</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O HORIZON LINES, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>4064 COLONY ROAD, SUITE 200</rptOwnerStreet2>
            <rptOwnerCity>CHARLOTTE</rptOwnerCity>
            <rptOwnerState>NC</rptOwnerState>
            <rptOwnerZipCode>28211</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $.01 per share</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5231</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Award of restircted shares of Common Stock, par value $0.01 per share, pursuant to the Issuer's Amended and Restated Equity Incentive Plan. 1,744 of these restricted shares vest on June 5, 2008 and the remaining 3,487 restricted shares vest on June 5, 2010.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Mike Avara, Attorney in Fact</signatureName>
        <signatureDate>2007-08-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
