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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-01-12</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001571498</issuerCik>
        <issuerName>Epizyme, Inc.</issuerName>
        <issuerTradingSymbol>EPZM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001110780</rptOwnerCik>
            <rptOwnerName>GOLDFISCHER CARL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>11 BELVEDERE AVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BELVEDERE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94920</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 $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2016-01-12</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>545166</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>9.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3370562</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2016-01-12</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10389</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>9.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3380951</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Reports the purchase of shares in the underwritten public offering of common stock of Epizyme, Inc.</footnote>
        <footnote id="F2">Represents shares held by Bay City Capital Fund V, L.P. (&quot;Fund V&quot;); and indirect interests of Bay City Capital (&quot;BCC&quot;), the manager of Bay City Capital Management V LLC (&quot;Management V&quot;), and Management V, the general partner of Fund V.  Dr. Goldfischer is Managing Director of BCC.  Dr. Goldfischer, BCC and Management V each disclaims beneficial ownership in such shares, except to the extent of their pecuniary interest therein.</footnote>
        <footnote id="F3">Represents shares held by Bay City Capital Fund V Co-Investment Fund, L.P. (&quot;Co-Investment V&quot;); and indirect interests of BCC, the manager of Management V, and Management V, the general partner of Fund V. Dr. Goldfischer is Managing Director of BCC. Dr. Goldfischer, BCC and Management V each disclaims beneficial ownership in such shares, except to the extent of their pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Carl Goldfischer</signatureName>
        <signatureDate>2016-01-12</signatureDate>
    </ownerSignature>
</ownershipDocument>
