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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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<SEC-DOCUMENT>0001209191-09-033726.txt : 20090625
<SEC-HEADER>0001209191-09-033726.hdr.sgml : 20090625
<ACCEPTANCE-DATETIME>20090625145917
ACCESSION NUMBER:		0001209191-09-033726
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20090619
FILED AS OF DATE:		20090625
DATE AS OF CHANGE:		20090625

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Flynn William J
		CENTRAL INDEX KEY:			0001364154

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-32627
		FILM NUMBER:		09909518

	MAIL ADDRESS:	
		STREET 1:		C/O ATLAS AIR WORLDWIDE HOLDINGS, INC.
		STREET 2:		2000 WESTCHESTER AVENUE
		CITY:			PURCHASE
		STATE:			NY
		ZIP:			10577

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			Horizon Lines, Inc.
		CENTRAL INDEX KEY:			0001302707
		STANDARD INDUSTRIAL CLASSIFICATION:	WATER TRANSPORTATION [4400]
		IRS NUMBER:				000000000
		FISCAL YEAR END:			1221

	BUSINESS ADDRESS:	
		STREET 1:		4064 COLONY ROAD
		STREET 2:		SUITE 200
		CITY:			CHARLOTTE
		STATE:			NC
		ZIP:			28211
		BUSINESS PHONE:		704-973-7000

	MAIL ADDRESS:	
		STREET 1:		4064 COLONY ROAD
		STREET 2:		SUITE 200
		CITY:			CHARLOTTE
		STATE:			NC
		ZIP:			28211

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	H Lines Holding Corp
		DATE OF NAME CHANGE:	20040909
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-06-19</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001364154</rptOwnerCik>
            <rptOwnerName>Flynn William J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>4064 COLONY ROAD</rptOwnerStreet1>
            <rptOwnerStreet2>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>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.01 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2009-06-19</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>15235</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42907</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Award of restricted shares of Common Stock, par value $0.01 per share, pursuant to the Issuer's 2009 Incentive Compensation Plan. These restricted shares vest on June 19, 2010.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Robert S. Zuckerman, Attorney-in-Fact</signatureName>
        <signatureDate>2009-06-25</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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