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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2022-10-19</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001645842</issuerCik>
        <issuerName>Zymergen Inc.</issuerName>
        <issuerTradingSymbol>ZY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001836869</rptOwnerCik>
            <rptOwnerName>SVF Excalibur (Cayman) Ltd</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O WALKERS CORP LTD., 190 ELGIN AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GEORGE TOWN</rptOwnerCity>
            <rptOwnerState>E9</rptOwnerState>
            <rptOwnerZipCode>KY1-9008</rptOwnerZipCode>
            <rptOwnerStateDescription>CAYMAN ISLANDS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001782338</rptOwnerCik>
            <rptOwnerName>SVF Endurance (Cayman) Ltd</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O WALKERS CORP LTD., 190 ELGIN AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GEORGE TOWN</rptOwnerCity>
            <rptOwnerState>E9</rptOwnerState>
            <rptOwnerZipCode>KY1-9008</rptOwnerZipCode>
            <rptOwnerStateDescription>CAYMAN ISLANDS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001731509</rptOwnerCik>
            <rptOwnerName>SB INVESTMENT ADVISERS (UK) LTD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>69 GROSVENOR STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>LONDON</rptOwnerCity>
            <rptOwnerState>X0</rptOwnerState>
            <rptOwnerZipCode>W1K 3JP</rptOwnerZipCode>
            <rptOwnerStateDescription>UNITED KINGDOM</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001755143</rptOwnerCik>
            <rptOwnerName>SOFTBANK VISION FUND (AIV M1) L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>251 LITTLE FALLS DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WILMINGTON</rptOwnerCity>
            <rptOwnerState>DE</rptOwnerState>
            <rptOwnerZipCode>19808</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2022-10-19</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>26614219</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Pursuant to the Merger Agreement, dated July 24, 2022 (the &quot;Merger Agreement&quot;), by and among the Issuer, Ginkgo Bioworks Holdings, Inc. (&quot;Ginkgo&quot;) and Pepper Merger Subsidiary Inc., the Issuer became an indirect wholly owned subsidiary of Ginkgo upon consummation of the merger on October 19, 2022 (the &quot;Effective Time&quot;), as provided for in the Merger Agreement. At the Effective Time, each share of the Issuer's common stock was automatically cancelled, extinguished and converted into the right to receive 0.9179 shares of Class A common stock of Ginkgo, with fractional shares paid in cash, without interest.</footnote>
        <footnote id="F2">The securities reported herein are held of record by SVF Excalibur (Cayman) Limited, which is a wholly owned subsidiary of SVF Endurance (Cayman) Limited, which is a wholly owned subsidiary of SoftBank Vision Fund (AIV M1) L.P. SB Investment Advisers (UK) Limited has been appointed as alternative investment fund manager (&quot;AIFM&quot;) and is exclusively responsible for managing SoftBank Vision Fund (AIV M1) L.P. in accordance with the Alternative Investment Fund Managers Directive and is authorized and regulated by the UK Financial Conduct Authority accordingly.</footnote>
        <footnote id="F3">As AIFM of SoftBank Vision Fund (AIV M1) L.P., SB Investment Advisers (UK) Limited is exclusively responsible for making all decisions related to the acquisition, structuring, financing and disposal of SoftBank Vision Fund (AIV M1) L.P.'s investments. As a result, each of the reporting persons may be deemed to share beneficial ownership of the securities reported herein, but disclaims beneficial ownership except to the extent of the pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>SVF Excalibur (Cayman) Limited By: /s/ Jonathan Duckles, Director</signatureName>
        <signatureDate>2022-10-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>SVF Endurance (Cayman) Limited By: /s/ Jonathan Duckles, Director</signatureName>
        <signatureDate>2022-10-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>SoftBank Vision Fund (AIV M1) L.P., By: SB Investment Advisers (UK) Limited, its manager, By: /s/ Amanda Sanchez-Barry, General Counsel</signatureName>
        <signatureDate>2022-10-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>SB Investment Advisers (UK) Limited By: /s/ Amanda Sanchez-Barry, General Counsel</signatureName>
        <signatureDate>2022-10-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
