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    <submissionType>D</submissionType>

    <testOrLive>LIVE</testOrLive>

    <primaryIssuer>
        <cik>0001411690</cik>
        <entityName>BioNano Genomics, Inc</entityName>
        <issuerAddress>
            <street1>9640 TOWNE CENTRE DRIVE</street1>
            <city>SAN DIEGO</city>
            <stateOrCountry>CA</stateOrCountry>
            <stateOrCountryDescription>CALIFORNIA</stateOrCountryDescription>
            <zipCode>92121</zipCode>
        </issuerAddress>
        <issuerPhoneNumber>(858) 888-7600</issuerPhoneNumber>
        <jurisdictionOfInc>DELAWARE</jurisdictionOfInc>
        <edgarPreviousNameList>
            <previousName>BioNanomatrix Inc</previousName>
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        <entityType>Corporation</entityType>
        <yearOfInc>
            <withinFiveYears>true</withinFiveYears>
            <value>2007</value>
        </yearOfInc>
    </primaryIssuer>

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                <firstName>R.</firstName>
                <middleName>Erik</middleName>
                <lastName>Holmlin</lastName>
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                <street1>c/o BioNano Genomics, Inc.</street1>
                <street2>9640 Towne Centre Drive, Suite 100</street2>
                <city>San Diego</city>
                <stateOrCountry>CA</stateOrCountry>
                <stateOrCountryDescription>CALIFORNIA</stateOrCountryDescription>
                <zipCode>92121</zipCode>
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                <relationship>Director</relationship>
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        </relatedPersonInfo>
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            <relatedPersonName>
                <firstName>David</firstName>
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                <stateOrCountryDescription>CALIFORNIA</stateOrCountryDescription>
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                <firstName>Albert</firstName>
                <middleName>A.</middleName>
                <lastName>Luderer</lastName>
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                <street1>c/o BioNano Genomics, Inc.</street1>
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        <relatedPersonInfo>
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                <lastName>Cao</lastName>
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        <relatedPersonInfo>
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                <firstName>Garth</firstName>
                <lastName>Monroe</lastName>
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                <zipCode>92121</zipCode>
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    <offeringData>
        <industryGroup>
            <industryGroupType>Pharmaceuticals</industryGroupType>
        </industryGroup>
        <issuerSize>
            <revenueRange>Decline to Disclose</revenueRange>
        </issuerSize>
        <federalExemptionsExclusions>
            <item>06</item>
        </federalExemptionsExclusions>
        <typeOfFiling>
            <newOrAmendment>
                <isAmendment>false</isAmendment>
            </newOrAmendment>
            <dateOfFirstSale>
                <value>2012-06-20</value>
            </dateOfFirstSale>
        </typeOfFiling>
        <durationOfOffering>
            <moreThanOneYear>false</moreThanOneYear>
        </durationOfOffering>
        <typesOfSecuritiesOffered>
            <isEquityType>true</isEquityType>
            <isOptionToAcquireType>true</isOptionToAcquireType>
            <isSecurityToBeAcquiredType>true</isSecurityToBeAcquiredType>
            <isOtherType>true</isOtherType>
            <descriptionOfOtherType>Securities offered consist of shares of convertible preferred stock, the convertible preferred stock issued upon exercise of the warrants and the common stock underlying the convertible preferred stock.</descriptionOfOtherType>
        </typesOfSecuritiesOffered>
        <businessCombinationTransaction>
            <isBusinessCombinationTransaction>false</isBusinessCombinationTransaction>
            <clarificationOfResponse></clarificationOfResponse>
        </businessCombinationTransaction>
        <minimumInvestmentAccepted>0</minimumInvestmentAccepted>
        <salesCompensationList></salesCompensationList>
        <offeringSalesAmounts>
            <totalOfferingAmount>13939494</totalOfferingAmount>
            <totalAmountSold>11573201</totalAmountSold>
            <totalRemaining>2366293</totalRemaining>
            <clarificationOfResponse>Amounts listed above include an aggregate of $2,787,501 receivable upon the exercise of warrants to purchase shares of convertible preferred stock.  Such warrants have not yet been exercised.</clarificationOfResponse>
        </offeringSalesAmounts>
        <investors>
            <hasNonAccreditedInvestors>false</hasNonAccreditedInvestors>
            <totalNumberAlreadyInvested>6</totalNumberAlreadyInvested>
        </investors>
        <salesCommissionsFindersFees>
            <salesCommissions>
                <dollarAmount>0</dollarAmount>
            </salesCommissions>
            <findersFees>
                <dollarAmount>0</dollarAmount>
            </findersFees>
            <clarificationOfResponse></clarificationOfResponse>
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        <useOfProceeds>
            <grossProceedsUsed>
                <dollarAmount>0</dollarAmount>
            </grossProceedsUsed>
            <clarificationOfResponse></clarificationOfResponse>
        </useOfProceeds>
        <signatureBlock>
            <authorizedRepresentative>false</authorizedRepresentative>
            <signature>
                <issuerName>BioNano Genomics, Inc</issuerName>
                <signatureName>Garth Monroe</signatureName>
                <nameOfSigner>Garth Monroe</nameOfSigner>
                <signatureTitle>CFO</signatureTitle>
                <signatureDate>2012-06-29</signatureDate>
            </signature>
        </signatureBlock>
    </offeringData>
</edgarSubmission>
