<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-07-11</periodOfReport>
    <issuer>
        <issuerCik>0000077551</issuerCik>
        <issuerName>APPLERA CORP</issuerName>
        <issuerTradingSymbol>ABI/CRA</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId>
            <rptOwnerCik>0001171315</rptOwnerCik>
            <rptOwnerName>WHITE TONY L</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>Chairman, President and CEO</officerTitle></reportingOwnerRelationship></reportingOwner><nonDerivativeSecurity><securityTitle><value>Applied Biosystems Group Common Stock</value></securityTitle><transactionDate><value>2003-07-11</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>15780</value></transactionShares><transactionValue><value>19.695</value><footnoteId id="F1"/></transactionValue><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>492427.0265</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity><nonDerivativeSecurity><securityTitle><value>Applied Biosystems Group Common Stock</value></securityTitle><transactionDate><value>2003-07-11</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>15780</value></transactionShares><transactionValue><value>19.695</value><footnoteId id="F1"/></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>476647.0265</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity><derivativeSecurity><securityTitle><value>Applied Biosystems Group Series FY03-3 Performance Units</value></securityTitle><conversionOrExercisePrice><value>0</value><footnoteId id="F2"/></conversionOrExercisePrice><transactionDate><value>2003-07-11</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>20000</value><footnoteId id="F3"/></transactionShares><transactionValue><value>0</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1988-08-08</value><footnoteId id="F2"/></exerciseDate><expirationDate><value>2013-03-24</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Applied Biosystems Group Common Stock</value><footnoteId id="F2"/></underlyingSecurityTitle><underlyingSecurityShares><value>20000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>20000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><footnotes><footnote id="F1">Represents settlement of Performance Units for cash as described in footnote 3 below.  Price listed is the fair market value of Applera Corporation - Applied Biosystems Group Common Stock (&amp;quot;ABI Stock&amp;quot;) on the settlement date.</footnote><footnote id="F2">The Performance Units provide for payment upon ABI Stock attaining price targets of $18.54 and $22.29 per share for a specified period and are payable over a minimum of eight quarters, subject to continued employment and an aggregate program expense cap.  Units are payable in cash or ABI Stock equal to $15.54 for each Performance Unit.</footnote><footnote id="F3">Represents the payment of 20,000 Performance Units upon attainment of $18.54 price target described in footnote 2 above.</footnote></footnotes><ownerSignature><signatureName>Thomas P. Livingston, Attorney-In-Fact for Tony L. White</signatureName><signatureDate>2003-07-15</signatureDate></ownerSignature></ownershipDocument>

