-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 NlmTq4wdxIJjCqDZ+5jKOyXwZtaflOZb517X8ljVOu5SVCXNft7ewclfIq3gQYpx
 HUoO2o/ca9Cr5YXKFV/lLg==

<SEC-DOCUMENT>0000077551-06-000123.txt : 20061207
<SEC-HEADER>0000077551-06-000123.hdr.sgml : 20061207
<ACCEPTANCE-DATETIME>20061207163456
ACCESSION NUMBER:		0000077551-06-000123
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20061206
FILED AS OF DATE:		20061207
DATE AS OF CHANGE:		20061207

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			WHITE TONY L
		CENTRAL INDEX KEY:			0001171315

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-04389
		FILM NUMBER:		061263038

	BUSINESS ADDRESS:	
		STREET 1:		C/O APPLERA CORPORATION
		STREET 2:		301 MERRITT 7
		CITY:			NORWALK
		STATE:			CT
		ZIP:			06851

	MAIL ADDRESS:	
		STREET 1:		C/O APPLERA CORP
		STREET 2:		301 MERRITT 7, PO BOX 5435
		CITY:			NORWALK
		STATE:			CT
		ZIP:			06856-5435

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
</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>2006-12-06</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>APPLERA CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>301 MERRITT 7</rptOwnerStreet2>
            <rptOwnerCity>NORWALK</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06851-1070</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chairman, President and CEO</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Applied Biosystems Group Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-12-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>13328</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>37.515</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>709614.2486</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Applied Biosystems Group Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-12-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>13328</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>37.515</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>696286.2486</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Applied Biosystems Group Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>75000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Elizabeth Ann White Business Interests, LLLP</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Applied Biosystems Group Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>63000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tony Lee White 2006 Two Year Grantor Retained Annuity Trust</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Applied Biosystems Group Series FY02-1 Performance Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-12-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>20000</value>
                    <footnoteId id="F5"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-08-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Applied Biosystems Group Common Stock</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Represents settlement of Performance Units for cash as described in footnote 5 below.  Price listed is the fair market value of Applera Corporation - Applied Biosystems Group Common Stock (&quot;ABI Stock&quot;) on the settlement date.</footnote>
        <footnote id="F2">Elizabeth Ann White Business Interests, LLLP, is a family limited partnership (the &quot;FLP&quot;).  The reporting person's adult daughter is the sole general partner of the FLP, and the reporting person's wife and a grantor retained annuity trust established by the reporting person are currently the sole limited partners of the FLP.</footnote>
        <footnote id="F3">The reporting person's wife is the sole trustee of the Tony Lee White 2006 Two Year Grantor Retained Annuity Trust.</footnote>
        <footnote id="F4">The Performance Units provide for payment upon ABI Stock attaining price targets of $30.00 and $35.00 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 equal to $25.00 for each Performance Unit.</footnote>
        <footnote id="F5">Represents the payment of 20,000 Performance Units upon attainment of the $35.00 price target described in footnote 4 above.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas P. Livingston, Attorney-in-Fact for Tony L. White</signatureName>
        <signatureDate>2006-12-07</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----