EXHIBIT
  31.1

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CERTIFICATION
OF PRINCIPAL EXECUTIVE OFFICER
PURSUANT TO EXCHANGE ACT RULE 13a-14(a)/15d-14(a),
AS ADOPTED PURSUANT TO SECTION
302 OFTHE SARBANES-OXLEY ACT OF 2002

I, Tony L. White, certify that:

|1. | I have reviewed this annual report on Form 10-K of Applera Corporation;                                                                                                                                                                                                                                                 
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|2. | Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;              
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|3. | Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;                                 
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|4. | The registrants other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:                                                                                          
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|   | (a)                                                                                                                                                                                                                                                                                                                     
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|   | (b)                                                                                                                                                                                                                                                                                                                     
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|   | (c)                                                                                                                                                                                                                                                                                                                     
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|5. | The
      registrants other certifying officer(s) and I have disclosed, based
      on our most recent evaluation of internal control over financial reporting,
      to the registrants auditors and the audit committee of the registrants
    board of directors (or persons performing the equivalent functions):
|   |                                                                                                                                                                                                                                                                                                                         
|   | (a)                                                                                                                                                                                                                                                                                                                     



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| | (b) | Any
        fraud, whether or not material, that involves management or other employees
        who have a significant role in the registrants internal control
    over financial reporting.
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Date: September
9, 2004

| | /s/ Tony
    L. White      
| | ---------------------------
| |                            
| | Chief
    Executive Officer

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