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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2014-08-22</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001368993</issuerCik>
        <issuerName>WaferGen Bio-systems, Inc.</issuerName>
        <issuerTradingSymbol>WGBS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001044321</rptOwnerCik>
            <rptOwnerName>MARXE AUSTIN W &amp; GREENHOUSE DAVID M</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SPECIAL SITUATIONS FUNDS</rptOwnerStreet1>
            <rptOwnerStreet2>527 MADISON AVENUE, SUITE 2600</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1400000</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Limited Partnerships</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2014-08-22</value>
            </exerciseDate>
            <expirationDate>
                <value>2019-08-22</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1400000</value>
                    <footnoteId id="F2"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Limited Partnerships</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This is a joint filing by Austin W. Marxe (Marxe), David M. Greenhouse (Greenhouse) and Adam C. Stettner (Stettner).  They share voting and investment control over all securities owned by Special Situations Fund III QP, L.P. (QP), Special Situations Cayman Fund, L.P. (Cayman), Special Situations Private Equity Fund, L.P. (PE) and Special Situations Life Sciences Fund, L.P. (LS), respectively.  600,000 shares of Common Stock are held by QP, 200,000 shares of Common Stock are held by Cayman, 200,000 shares of Common Stock are held by PE and 400,000 shares of Common Stock are held by LS. The interest of Marxe, Greenhouse and Stettner in the shares of Common Stock owned by QP, Cayman, PE, and LS is limited to the extent of his pecuniary interest.</footnote>
        <footnote id="F2">This is a joint filing by Austin W. Marxe (Marxe), David M. Greenhouse (Greenhouse) and Adam Stettner (Stettner).  They share voting and investment control over all securities owned by Special Situations Fund III QP, L.P. (QP), Special Situations Cayman Fund, LP (Cayman), Special Situations Private Equity Fund, L.P. (PE) and Special Situations Life Sciences Fund, L.P. (LS).  600,000 Warrants are held by QP, 200,000 Warrants are held by Cayman, 200,000 Warrants are held by PE and 400,000 Warrants are held by LS.  The interest of Marxe, Greenhouse and Stettner in the shares of warrants owned by QP, Cayman, PE and LS is limited to the extent of his pecuniary interest.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Austin W. Marxe</signatureName>
        <signatureDate>2014-08-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>David M. Greenhouse</signatureName>
        <signatureDate>2014-08-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Adam C. Stettner</signatureName>
        <signatureDate>2014-08-28</signatureDate>
    </ownerSignature>
</ownershipDocument>
