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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2013-02-27</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000730716</issuerCik>
        <issuerName>ZYGO CORP</issuerName>
        <issuerTradingSymbol>ZIGO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001385702</rptOwnerCik>
            <rptOwnerName>MAK CAPITAL ONE LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>590 MADISON AVENUE, 9TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></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>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001426156</rptOwnerCik>
            <rptOwnerName>MAK Capital Fund LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>590 MADISON AVENUE, 9TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></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>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001480092</rptOwnerCik>
            <rptOwnerName>MAK-ro Capital Master Fund LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O DUNDEE LEEDS MANAGEMENT SERVICES LTD</rptOwnerStreet1>
            <rptOwnerStreet2>129 FRONT STREET</rptOwnerStreet2>
            <rptOwnerCity>HAMILTON</rptOwnerCity>
            <rptOwnerState>D0</rptOwnerState>
            <rptOwnerZipCode>HM12</rptOwnerZipCode>
            <rptOwnerStateDescription>BERMUDA</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001044734</rptOwnerCik>
            <rptOwnerName>SUSSMAN S DONALD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>217 COMMERCIAL STREET</rptOwnerStreet1>
            <rptOwnerStreet2>5TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>PORTLAND</rptOwnerCity>
            <rptOwnerState>ME</rptOwnerState>
            <rptOwnerZipCode>04101</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001426157</rptOwnerCik>
            <rptOwnerName>Kaufman Michael A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>590 MADISON AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>9TH FLOOR</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>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2013-02-27</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>250000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.60</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>433890</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">Reflects the transactions of securities owned directly by MAK-ro Capital Master Fund LP (the &quot;MAK-ro Fund&quot;).</footnote>
        <footnote id="F2">MAK Capital  Fund LP (&quot;MAK Capital Fund&quot;) directly owns 3,073,785  shares of common stock.  Paloma International L.P. (&quot;Paloma&quot;) through its subsidiary, Sunrise Partners Limited Partnership, directly owns 740,183 shares of common stock.  MAK Capital One LLC (&quot;MAK Capital One&quot;) acts as the investment manager of MAK Capital Fund, MAK-ro Fund and Paloma with respect to the securities reported herein.  Michael A. Kaufman is the managing member of MAK Capital One and the controlling person of MAK Capital Fund and MAK-ro Fund.  S. Donald Sussman is the controlling person of Paloma.</footnote>
        <footnote id="F3">MAK Capital One and Michael A. Kaufman may be deemed to indirectly beneficially own the shares of common stock held by MAK Capital Fund, MAK-ro Fund and Paloma.  Mr. Sussman may be deemed to indirectly beneficially own the shares of common stock held by Paloma.  For purposes of this Form 4, MAK Capital One, Mr. Kaufman and Mr. Sussman each disclaims beneficial ownership of the shares of common stock owned by MAK Capital Fund, MAK-ro Fund and Paloma, except to the extent of their pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Michael A. Kaufman, Managing Member of MAK CAPITAL ONE LLC</signatureName>
        <signatureDate>2013-03-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
