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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2019-03-31</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001184592</rptOwnerCik>
            <rptOwnerName>SEIDENBERG BETH C</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>2750 SAND HILL ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</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</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <transactionDate>
                <value>2019-03-31</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1024</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>12.39</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7471</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $0.0001</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4115555</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Notes 2 and 3</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>13.74</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2019-05-31</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>17633</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2029-05-30</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>17633</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>17633</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares were issued to the Reporting Person pursuant to her election under the Company's director compensation program to receive such shares in lieu of cash fees of $12,687.50 for Board services for the first fiscal quarter of 2019.  The shares were issued on the last day of the first fiscal quarter and the number of shares was calculated by dividing the cash fees to be paid for the quarter by the closing price of the Company's common stock on the last trading day of the quarter.</footnote>
        <footnote id="F2">The shares consist of 3,838,167 shares of common stock held by Kleiner Perkins Caufield &amp; Byers XIII, LLC (&quot;KPCB XIII&quot;) and 277,388 shares of common stock beneficially owned by individuals and entities associated with Kleiner Perkins Caulfield &amp; Byers (collectively, &quot;KPCB Direct&quot;). All shares are held for convenience in the name of &quot;KPCB Holdings, Inc., as nominee,&quot; for the accounts of such individuals and entities who each exercise their own voting and dispositive control over such shares. The managing member of KPCB XIII is KPCB XIII Associates, LLC, which has sole voting and dispositive power over the shares held by KPCB XIII. The Reporting Person disclaims beneficial ownership of all shares held by KPCB XIII except to the extent of her pecuniary interest therein.</footnote>
        <footnote id="F3">The Reporting Person disclaims beneficial ownership over all Issuer shares held for convenience in the name of &quot;KPCB Holdings, Inc. as nominee,&quot; except to the extent of her pecuniary interest therein and this filing is not an admission that the Reporting Person is the beneficial owner of these shares for the purposes of Section 16 or for any other purpose.</footnote>
        <footnote id="F4">This option will vest in full on May 31, 2020, subject to Reporting Person's continued service as a director.  In the event of a change in control of the Issuer, the option will become exercisable in full.</footnote>
    </footnotes>

    <remarks>Exhibit List
Exhibit 24 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>/s/ John Weidenbruch, attorney-in-fact</signatureName>
        <signatureDate>2019-06-07</signatureDate>
    </ownerSignature>
</ownershipDocument>
