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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2020-02-11</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001507678</rptOwnerCik>
            <rptOwnerName>Legorreta Pablo G.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RP MANAGEMENT, LLC,</rptOwnerStreet1>
            <rptOwnerStreet2>110 E. 59TH ST., 33RD FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001507673</rptOwnerCik>
            <rptOwnerName>RP Management, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RP MANAGEMENT, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>110 E. 59TH ST., 33RD FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001793690</rptOwnerCik>
            <rptOwnerName>RPI Finance Trust</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RP MANAGEMENT, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>110 E. 59TH ST., 33RD FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2020-02-11</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2500000</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>20.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>9166667</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>20.00</value>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2019-11-06</value>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2022-11-06</value>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2500000</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2500000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>13.51</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2029-11-05</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>34408</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>34408</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F6"/>
                    <footnoteId id="F7"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Represents 2,500,000 shares of the Issuer's common stock acquired by RPI Finance Trust (&quot;RPIFT&quot;) on February 11, 2020 pursuant to that certain Purchase Agreement, dated November 4, 2019, by and between the Issuer and RPIFT (the &quot;Purchase Agreement&quot;), whereby the Issuer had the option, subject to certain conditions, to sell $50 million of its common stock to RPIFT until May 6, 2021 at a maximum price of $20.00 per share. The Issuer exercised this option on December 30, 2019 and on February 11, 2020, the Issuer issued and sold to RPIFT 2,500,000 shares of its common stock at a price of $20.00 per share.</footnote>
        <footnote id="F2">This Form 4 is being jointly filed by RP Management, LLC (&quot;RP Management&quot;), RPIFT and Pablo G. Legorreta (collectively, the &quot;Reporting Persons&quot;). RP Management, as the manager of RPIFT, and Mr. Legorreta, as the manager of RP Management, may be deemed to have beneficial ownership under Section 13 of the Securities Exchange Act of 1934, as amended (the &quot;Exchange Act&quot;) of the securities beneficially owned by RPIFT. RP Management and Mr. Legorreta disclaim beneficial ownership of the securities indicated except to the extent of their pecuniary interest therein, and the reporting herein of such securities shall not be construed as an admission that RP Management and/or Mr. Legorreta are the beneficial owners thereof for purposes of Section 16 of the Exchange Act or for any other purpose. Mr. Legorreta serves on the board of directors of the Issuer as a representative of RPIFT.</footnote>
        <footnote id="F3">(Continued from Footnote 2) Each of RPIFT and RP Management, LLC may be deemed to be a director by deputization of the Issuer for purposes of Section 16(b)-3(d) of the Exchange Act.</footnote>
        <footnote id="F4">Pursuant to the terms of the Purchase Agreement, on November 6, 2019, RPIFT acquired a warrant to purchase up to 2,500,000 shares of the Issuer's common stock at a price of $20.00 per share, subject to adjustment in accordance with the terms thereof (the &quot;Warrant&quot;). The Warrant became immediately exercisable, in whole or in part, on November 6, 2019 and terminates on November 6, 2022.</footnote>
        <footnote id="F5">This option was granted to Mr. Legorreta on November 6, 2019 pursuant to the Issuer's 2013 Stock Incentive Plan with respect to 34,408 shares of common stock, in connection with Mr. Legorreta's election to the board of directors of the Issuer. This option vests as to 25% of the shares on the first anniversary of the grant date and as to an additional 2.0833% of the shares at the end of each successive month following the first anniversary of the grant date until the fourth anniversary of the grant date.</footnote>
        <footnote id="F6">Mr. Legorreta is deemed to hold the stock option and the shares issuable thereunder for the benefit of RP Management. Mr. Legorreta is the manager of RP Management. Any exercise of the stock option, when vested, or sale of the shares issuable upon exercise shall be at the direction of RP Management and the proceeds of the sale of the shares issuable upon exercise shall be delivered to RP Management. The proceeds of the sale of the shares issuable under the stock option will be offset against the management fee payable to RP Management by certain indirect owners (the &quot;Funds&quot;) of RPIFT, all of which are managed by RP Management.</footnote>
        <footnote id="F7">(Continued from Footnote 6) Mr. Legorreta and such Funds disclaim beneficial ownership of the securities indicated except to the extent of their pecuniary interest therein, and the reporting herein of such securities shall not be construed as an admission that Mr. Legorreta or any of such Funds is the beneficial owner thereof for purposes of Section 16 of the Exchange Act or for any other purpose. Mr. Legorreta serves on the board of directors of the Issuer as a representative of RPIFT. Each of RPIFT and RP Management may be deemed to be a director by deputization of the Issuer for purposes of Section 16(b)-3(d) of the Exchange Act.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Pablo G. Legorreta</signatureName>
        <signatureDate>2020-02-13</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>RP Management, LLC, By: /s/ Pablo G. Legorreta, Chief Executive Officer</signatureName>
        <signatureDate>2020-02-13</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>RPI Finance Trust, By: RP Management, LLC, its Administrator, /s/ Pablo G. Legorreta, Chief Executive Officer</signatureName>
        <signatureDate>2020-02-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
