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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2024-02-08</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001785279</issuerCik>
        <issuerName>Metagenomi, Inc.</issuerName>
        <issuerTradingSymbol>MGX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001388325</rptOwnerCik>
            <rptOwnerName>Novo Holdings A/S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TUBORG HAVNEVEJ 19</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>HELLERUP</rptOwnerCity>
            <rptOwnerState>G7</rptOwnerState>
            <rptOwnerZipCode>2900</rptOwnerZipCode>
            <rptOwnerStateDescription>DENMARK</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>SERIES B PREFERRED STOCK</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>147415</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>SERIES B-1 PREFERRED STOCK</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>691760</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each share of Series B Preferred Stock and Series B-1 Preferred Stock is convertible into Common Stock, on a one-for-one basis, automatically upon the closing of the Issuer's initial public offering without payment of additional consideration. These shares have no expiration date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Barbara Fiorini Due, General Counsel, Finance &amp; Operations</signatureName>
        <signatureDate>2024-02-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
