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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-09-11</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001701108</issuerCik>
        <issuerName>Spero Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>SPRO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001591986</rptOwnerCik>
            <rptOwnerName>Aquilo Capital Management, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE LETTERMAN DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE D4900, BUILDING D</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94129</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001491371</rptOwnerCik>
            <rptOwnerName>Aquilo Capital, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE LETTERMAN DRIVE, SUITE D4900</rptOwnerStreet1>
            <rptOwnerStreet2>BUILDING D, THE PRESIDIO</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94129</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, $0.001 Par Value</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4497142</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The reporting persons are Aquilo Capital, L.P. (the &quot;Fund&quot;), Aquilo Capital Management, LLC (&quot;Aquilo&quot;) and Marc R. Schneidman. Aquilo is the general partner and investment adviser of the Fund that holds securities directly for the benefit of their investors. Aquilo may be deemed to beneficially own such securities indirectly as the investment adviser and general partner of the Fund, and Mr. Schneidman may be deemed to beneficially own them indirectly as the control person of Aquilo. Each of Aquilo, the Fund and Mr. Schneidman disclaims beneficial ownership of such securities except to the extent of his or its pecuniary interest therein.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Aquilo Capital Management, LLC By: Managing Member /s/ Marc Schneidman</signatureName>
        <signatureDate>2020-09-22</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Aquilo Capital, L.P., By: Aquilo Capital Management, LLC, its General Partner By: Marc Schneidman, its Managing Member /s/ Marc Schneidman</signatureName>
        <signatureDate>2020-09-22</signatureDate>
    </ownerSignature>
</ownershipDocument>
