-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 zFPwMKjVVrsJY5M4bV7NrQ==

<SEC-DOCUMENT>0000077551-05-000027.txt : 20050611
<SEC-HEADER>0000077551-05-000027.hdr.sgml : 20050611
<ACCEPTANCE-DATETIME>20050603170611
ACCESSION NUMBER:		0000077551-05-000027
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20050602
FILED AS OF DATE:		20050603
DATE AS OF CHANGE:		20050603

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			APPLERA CORP
		CENTRAL INDEX KEY:			0000077551
		STANDARD INDUSTRIAL CLASSIFICATION:	LABORATORY ANALYTICAL INSTRUMENTS [3826]
		IRS NUMBER:				061534213
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			0630

	BUSINESS ADDRESS:	
		STREET 1:		301 MERRITT 7
		CITY:			NORWALK
		STATE:			CT
		ZIP:			06851
		BUSINESS PHONE:		2038402000

	MAIL ADDRESS:	
		STREET 1:		301 MERRITT 7
		CITY:			NORWALK
		STATE:			CT
		ZIP:			06851

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	PE CORP
		DATE OF NAME CHANGE:	19990129

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	PERKIN ELMER CORP
		DATE OF NAME CHANGE:	19930601

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			DEBLASI UGO D
		CENTRAL INDEX KEY:			0001222640

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-04389
		FILM NUMBER:		05878367

	BUSINESS ADDRESS:	
		STREET 1:		APPLERA CORP, CELERA GEOMICS GROUP
		STREET 2:		45 WEST GUDE DR
		CITY:			ROCKVILLE
		STATE:			MD
		ZIP:			20850
		BUSINESS PHONE:		2404533000
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2005-06-02</periodOfReport>

    <issuer>
        <issuerCik>0000077551</issuerCik>
        <issuerName>APPLERA CORP</issuerName>
        <issuerTradingSymbol>ABI/CRA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001222640</rptOwnerCik>
            <rptOwnerName>DEBLASI UGO D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>APPLERA CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>301 MERRITT 7</rptOwnerStreet2>
            <rptOwnerCity>NORWALK</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06851</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Vice President and Controller</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Applied Biosystems Group Employee Stock Options-Right to Buy</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>21.475</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-06-02</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>28000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>21.475</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-06-02</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-06-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Applied Biosystems Group Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>28000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>28000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Celera Genomics Group Employee Stock Options-Right to Buy</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.155</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-06-02</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>10500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.155</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-06-02</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-06-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Celera Genomics Group Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>10500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These options are fully vested and exercisable as of the grant date.  However, shares acquired upon the exercise of these options are subject to a restriction on transfer (covering sales, gifts, pledges, and any other method of disposition).  The transfer restriction will lapse on 25% of the shares covered by the grant on each of the first four anniversaries of the grant date.  Also, the transfer restriction will lapse in full upon termination of employment for any reason.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas P. Livingston, Attorney-In-Fact for Ugo D. DeBlasi</signatureName>
        <signatureDate>2005-06-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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