<?xml version="1.0"?>
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    <periodOfReport>2021-11-17</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001830214</issuerCik>
        <issuerName>Ginkgo Bioworks Holdings, Inc.</issuerName>
        <issuerTradingSymbol>DNA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001873523</rptOwnerCik>
            <rptOwnerName>Shetty Reshma P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O GINKGO BIOWORKS HOLDINGS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>27 DRYDOCK AVENUE</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02210</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

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                    <value>By The Asha S. Canton Irrevocable Trust</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Class B Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <footnoteId id="F2"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1291794</value>
                    <footnoteId id="F5"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By The Adhira S. Canton Irrevocable Trust</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Represents the conversion of shares of Class B Common Stock to shares of Class A Common Stock.</footnote>
        <footnote id="F2">Shares of the Class B Common Stock may be converted into shares of Class A Common Stock, on a one-to-one basis, at the option of the holder at any time and have no expiration date.</footnote>
        <footnote id="F3">Represents restricted stock units (the &quot;RSUs&quot;) granted prior to the business combination of Soaring Eagle Acquisition Corp. and Ginkgo Bioworks, Inc. in September 2021 (the &quot;Merger&quot;), which became contingent rights to acquire equity securities of the Issuer upon consummation of the Merger. At the time of grant, the RSUs were subject to both a service-based vesting condition and a performance-based vesting condition.  On November 17, 2021, the board of directors of the Issuer modified the vesting terms of RSUs, such that the Merger was deemed to have satisfied the performance condition for vesting effective as of March 15, 2022.   The service-based vesting condition was satisfied on October 1, 2022, and the Issuer elected to deliver one share of Class A Common Stock for each RSU.  Such shares of Class A Common Stock may be exchanged for shares of Class B Common Stock.</footnote>
        <footnote id="F4">Represents the number of shares sold by the Reporting Person or the Reporting Person's spouse to cover tax withholding obligations in connection with the vesting of RSUs.  Sales to cover tax withholding obligations in connection with the vesting of such securities do not represent discretionary trades by the Reporting Person or the Reporting Person's spouse. The Issuer's equity incentive plans allow the Issuer to require that satisfaction of tax withholding obligation to be funded by a &quot;sell to cover&quot; transaction.</footnote>
        <footnote id="F5">Includes shares of Class B Common Stock that are subject to vesting conditions.</footnote>
    </footnotes>

    <remarks>President, COO &amp; Founder</remarks>

    <ownerSignature>
        <signatureName>/s/ Karen Tepichin, Attorney-in-Fact</signatureName>
        <signatureDate>2022-10-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
