<PAGE>

                                              Registration No. 333-

================================================================================
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   ----------

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                                   ----------

                               APPLERA CORPORATION
             (Exact Name of Registrant as Specified in Its Charter)


          Delaware                                          06-1534213
(State or Other Jurisdiction of                          (I.R.S. Employer
Incorporation or Organization)                         Identification Number)

                                  301 MERRITT 7
                         NORWALK, CONNECTICUT 06851-1070
          (Address of Principal Executive Offices, including Zip Code)

                                   ----------

                  APPLERA CORPORATION/APPLIED BIOSYSTEMS GROUP
                            1999 STOCK INCENTIVE PLAN
                            (Full Title of the Plan)

                                   ----------

                                WILLIAM B. SAWCH
                    Senior Vice President and General Counsel
                               APPLERA CORPORATION
                                  301 Merritt 7
                         Norwalk, Connecticut 06851-1070
                                 (203) 840-2000
           (Name, Address, and Telephone Number of Agent for Service)



                         CALCULATION OF REGISTRATION FEE
<TABLE>
<CAPTION>
====================================================================================================================================
                                                                            Proposed
                                                                            Maximum              Proposed Maximum
                                                     Amount to be      Offering Price Per       Aggregate Offering      Amount of
  Title of Securities to be Registered            Registered (1)(2)         Share (3)                Price (3)      Registration Fee
------------------------------------------------------------------------------------------------------------------------------------
<S>                                                  <C>                   <C>                    <C>                  <C>
Applera Corporation - Applied Biosystems Group       4,000,000              $20.05                $80,200,000          $7,379
  Common Stock, par value $.01 per share (2)
====================================================================================================================================
</TABLE>

1.    Together with an indeterminate number of additional shares that may be
      issued to adjust the number of shares reserved for issuance pursuant to
      the Applera Corporation/Applied Biosystems Group 1999 Stock Incentive Plan
      as the result of any future stock split, stock dividend, or similar
      adjustment to the Applera Corporation - Applied Biosystems Group Common
      Stock (the "Applera - Applied Biosystems Stock").
2.    This Registration Statement also includes rights to purchase Series A
      Participating Junior Preferred Stock, par value $.01 per share, of the
      Registrant (the "Rights"). Until the occurrence of certain prescribed
      events, the Rights are not exercisable, are evidenced by the certificates
      for Applera - Applied Biosystems Stock, and will be transferred along with
      and only with such securities. Thereafter, separate Rights certificates
      will be issued representing one Right for each share of Applera - Applied
      Biosystems Stock held, subject to adjustment pursuant to anti-dilution
      provisions.
3.    Pursuant to Rule 457(h)(1) and Rule 457(c), the proposed maximum offering
      price per share and the registration fee are based on the reported average
      of the high and low prices for the Applera - Applied Biosystems Stock on
      the New York Stock Exchange on December 10, 2002. The maximum offering
      price per share is estimated solely for purposes of calculating the
      registration fee.
================================================================================
<PAGE>

      The contents of the Registration Statement on Form S-8 filed by Applera
Corporation (formerly PE Corporation) (the "Company") (File No. 333-82679) on
July 12, 1999, with the Securities and Exchange Commission pursuant to the
Securities Act of 1933, as amended, are hereby incorporated by reference in this
Registration Statement.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 5.  Interests of Named Experts and Counsel.

      Legal matters in connection with the shares of Applera - Applied
Biosystems Stock subject to issuance pursuant to the Applera Corporation/Applied
Biosystems Group 1999 Stock Incentive Plan have been passed upon by Thomas P.
Livingston, Esq., Secretary of the Company. Mr. Livingston owns Applera -
Applied Biosystems Stock and options to purchase Applera - Applied Biosystems
Stock with an aggregate value in excess of $50,000.

Item 8.    Exhibits.

      The following exhibits are filed as part of this Registration Statement:

Exhibit 3.1       Restated Certificate of Incorporation of Applera Corporation
                  (incorporated by reference to Exhibit 3(i) to the Company's
                  Quarterly Report on Form 10-Q for the fiscal quarter ended
                  December 31, 2000 (Commission File No. 1-4389)).

Exhibit 3.2       Bylaws of Applera Corporation (incorporated by reference to
                  Exhibit 3.2 to the Company's Registration Statement on
                  Form S-4 (Commission File No. 333-67797)).

Exhibit 3.3       Certificate of Designations of Series A Participating Junior
                  Preferred Stock and Series B Participating Junior Preferred
                  Stock (incorporated by reference to Exhibit A to Exhibit 4.1
                  to the Company's Registration Statement on Form S-4 (No.
                  333-67797)).

Exhibit 4.1       Stockholder Protection Rights Agreement, dated as of April 28,
                  1999, between Applera Corporation and BankBoston N.A.
                  (incorporated by reference to Exhibit 4.1 to the Company's
                  Registration Statement on Form S-4 (No. 333-67797)).

Exhibit 4.2       Amendment to Rights Agreement dated as of April 17, 2002,
                  among BankBoston, N.A., EquiServe Trust Company, N.A., and the
                  Company (incorporated by reference to Exhibit 4.2 to the
                  Company's Annual Report on Form 10-K for the fiscal year ended
                  June 30, 2002 (Commission file number 1-4389)).


                                       2
<PAGE>

Exhibit 5         Opinion of Thomas P. Livingston, Esq. (including consent).

Exhibit 10.1      Applera Corporation/Applied Biosystems Group 1999 Stock
                  Incentive Plan, as amended October 17, 2002 (incorporated by
                  reference to Appendix B to Schedule 14A, filed September 6,
                  2002, containing the Company's definitive Proxy Statement for
                  its 2002 Annual Meeting of Stockholders (Commission file
                  number 1-4389)).

Exhibit 23.1      Consent of PricewaterhouseCoopers LLP.

Exhibit 23.2      Consent of Thomas P. Livingston, Esq. (included in Exhibit 5).

Exhibit 24        Power of Attorney (contained on the signature pages hereof).


                                       3
<PAGE>

                                   SIGNATURES

      Pursuant to the requirements of the Securities Act of 1933, the Company
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Norwalk, State of Connecticut, on December 13, 2002.

                                        APPLERA CORPORATION


                                        By: /s/ William B. Sawch
                                            ------------------------------------
                                            William B. Sawch
                                            Senior Vice President and
                                            General Counsel


                                POWER OF ATTORNEY

      We, the undersigned directors and officers of the Company, do hereby
constitute and appoint Dennis L. Winger and William B. Sawch, or either of them,
our true and lawful attorneys and agents, to do any and all acts and things in
our name and on our behalf in our capacities as directors and officers and to
execute any and all instruments for us and in our names in the capacities
indicated below, which said attorneys and agents, or either of them, may deem
necessary or advisable to enable said corporation to comply with the Securities
Act of 1933 and any rules, regulations and requirements of the Securities and
Exchange Commission, in connection with this Registration Statement, including
specifically, but without limitation, power and authority to sign for us or any
of us in our names in the capacities indicated below, any and all amendments
(including post-effective amendments) hereto and we do hereby ratify and confirm
all that said attorneys and agents, or either of them, shall do or cause to be
done by virtue hereof.

      Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.

<TABLE>
<S>                                         <C>                                 <C>
      /s/ Tony L. White                     Chairman of the Board,              December 13, 2002
------------------------------------        President and
Tony L. White                               Chief Executive Officer
                                            (Principal Executive Officer)


</TABLE>


                                       4
<PAGE>

<TABLE>
<CAPTION>

<S>                                        <C>                                 <C>
      /s/ Dennis L. Winger                  Senior Vice President and           December 13, 2002
------------------------------------        Chief Financial Officer
Dennis L. Winger                            (Principal Financial Officer)


      /s/ Vikram Jog                        Controller                          December 13, 2002
------------------------------------        (Principal Accounting Officer)
Vikram Jog


      /s/ Richard H. Ayers                   Director                           December 13, 2002
------------------------------------
Richard H. Ayers


      /s/ Jean-Luc Belingard                 Director                           December 13, 2002
------------------------------------
Jean-Luc Belingard


      /s/ Robert H. Hayes                    Director                           December 13, 2002
------------------------------------
Robert H. Hayes


      /s/ Arnold J. Levine                   Director                           December 13, 2002
------------------------------------
Arnold J. Levine


      /s/ Theodore E. Martin                 Director                           December 13, 2002
------------------------------------
Theodore E. Martin


      /s/ Carolyn W. Slayman                 Director                           December 13, 2002
------------------------------------
Carolyn W. Slayman


      /s/ Orin R. Smith                      Director                           December 13, 2002
------------------------------------
Orin R. Smith


      /s/ Georges C. St. Laurent, Jr.        Director                           December 13, 2002
-------------------------------------
Georges C. St. Laurent, Jr.


      /s/ James R. Tobin                     Director                           December 13, 2002
-------------------------------------
James R. Tobin
</TABLE>


                                       5
<PAGE>

                                  EXHIBIT INDEX


Exhibit No.                        Description
-----------                        -----------

Exhibit 5         Opinion of Thomas P. Livingston, Esq. (including consent).

Exhibit 23.1      Consent of PricewaterhouseCoopers LLP.

Exhibit 23.2      Consent of Thomas P. Livingston, Esq. (included in Exhibit 5).

Exhibit 24        Power of Attorney (contained on the signature pages hereof).


                              6
[{"type": "S-8", "sequence": "1", "filename": "b321775_s8.txt", "description": "FORM S-8", "secsgml_size_bytes": 12982}]
{"company-data": {"conformed-name": "APPLERA CORP", "cik": "0000077551", "assigned-sic": "3826", "irs-number": "061534213", "state-of-incorporation": "DE", "fiscal-year-end": "0630"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-101846", "film-number": "02857447"}, "business-address": {"street1": "301 MERRITT 7", "city": "NORWALK", "state": "CT", "zip": "06851", "phone": "2038402000"}, "mail-address": {"street1": "301 MERRITT 7", "city": "NORWALK", "state": "CT", "zip": "06851"}, "former-company": [{"former-conformed-name": "PERKIN ELMER CORP", "date-changed": "19930601"}, {"former-conformed-name": "PE CORP", "date-changed": "19990129"}]}
Registration No. 333-

================================================================================
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   ----------

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                                   ----------

                               APPLERA CORPORATION
             (Exact Name of Registrant as Specified in Its Charter)

          Delaware                                          06-1534213
(State or Other Jurisdiction of                          (I.R.S. Employer
Incorporation or Organization)                         Identification Number)

                                  301 MERRITT 7
                         NORWALK, CONNECTICUT 06851-1070
          (Address of Principal Executive Offices, including Zip Code)

                                   ----------

                  APPLERA CORPORATION/APPLIED BIOSYSTEMS GROUP
                            1999 STOCK INCENTIVE PLAN
                            (Full Title of the Plan)

                                   ----------

                                WILLIAM B. SAWCH
                    Senior Vice President and General Counsel
                               APPLERA CORPORATION
                                  301 Merritt 7
                         Norwalk, Connecticut 06851-1070
                                 (203) 840-2000
           (Name, Address, and Telephone Number of Agent for Service)

                         CALCULATION OF REGISTRATION FEE
====================================================================================================================================
                                                                            Proposed
                                                                            Maximum              Proposed Maximum
                                                     Amount to be      Offering Price Per       Aggregate Offering      Amount of
  Title of Securities to be Registered            Registered (1)(2)         Share (3)                Price (3)      Registration Fee
------------------------------------------------------------------------------------------------------------------------------------
Applera Corporation - Applied Biosystems Group       4,000,000              $20.05                $80,200,000          $7,379
  Common Stock, par value $.01 per share (2)
====================================================================================================================================
1.    Together with an indeterminate number of additional shares that may be
      issued to adjust the number of shares reserved for issuance pursuant to
      the Applera Corporation/Applied Biosystems Group 1999 Stock Incentive Plan
      as the result of any future stock split, stock dividend, or similar
      adjustment to the Applera Corporation - Applied Biosystems Group Common
      Stock (the "Applera - Applied Biosystems Stock").
2.    This Registration Statement also includes rights to purchase Series A
      Participating Junior Preferred Stock, par value $.01 per share, of the
      Registrant (the "Rights"). Until the occurrence of certain prescribed
      events, the Rights are not exercisable, are evidenced by the certificates
      for Applera - Applied Biosystems Stock, and will be transferred along with
      and only with such securities. Thereafter, separate Rights certificates
      will be issued representing one Right for each share of Applera - Applied
      Biosystems Stock held, subject to adjustment pursuant to anti-dilution
      provisions.
3.    Pursuant to Rule 457(h)(1) and Rule 457(c), the proposed maximum offering
      price per share and the registration fee are based on the reported average
      of the high and low prices for the Applera - Applied Biosystems Stock on
      the New York Stock Exchange on December 10, 2002. The maximum offering
      price per share is estimated solely for purposes of calculating the
      registration fee.
================================================================================
The contents of the Registration Statement on Form S-8 filed by Applera
Corporation (formerly PE Corporation) (the "Company") (File No. 333-82679) on
July 12, 1999, with the Securities and Exchange Commission pursuant to the
Securities Act of 1933, as amended, are hereby incorporated by reference in this
Registration Statement.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 5.  Interests of Named Experts and Counsel.

      Legal matters in connection with the shares of Applera - Applied
Biosystems Stock subject to issuance pursuant to the Applera Corporation/Applied
Biosystems Group 1999 Stock Incentive Plan have been passed upon by Thomas P.
Livingston, Esq., Secretary of the Company. Mr. Livingston owns Applera -
Applied Biosystems Stock and options to purchase Applera - Applied Biosystems
Stock with an aggregate value in excess of $50,000.

Item 8.    Exhibits.

      The following exhibits are filed as part of this Registration Statement:

Exhibit 3.1       Restated Certificate of Incorporation of Applera Corporation
                  (incorporated by reference to Exhibit 3(i) to the Company's
                  Quarterly Report on Form 10-Q for the fiscal quarter ended
                  December 31, 2000 (Commission File No. 1-4389)).

Exhibit 3.2       Bylaws of Applera Corporation (incorporated by reference to
                  Exhibit 3.2 to the Company's Registration Statement on
                  Form S-4 (Commission File No. 333-67797)).

Exhibit 3.3       Certificate of Designations of Series A Participating Junior
                  Preferred Stock and Series B Participating Junior Preferred
                  Stock (incorporated by reference to Exhibit A to Exhibit 4.1
                  to the Company's Registration Statement on Form S-4 (No.
                  333-67797)).

Exhibit 4.1       Stockholder Protection Rights Agreement, dated as of April 28,
                  1999, between Applera Corporation and BankBoston N.A.
                  (incorporated by reference to Exhibit 4.1 to the Company's
                  Registration Statement on Form S-4 (No. 333-67797)).

Exhibit 4.2       Amendment to Rights Agreement dated as of April 17, 2002,
                  among BankBoston, N.A., EquiServe Trust Company, N.A., and the
                  Company (incorporated by reference to Exhibit 4.2 to the
                  Company's Annual Report on Form 10-K for the fiscal year ended
                  June 30, 2002 (Commission file number 1-4389)).

                                       2
Exhibit 5         Opinion of Thomas P. Livingston, Esq. (including consent).

Exhibit 10.1      Applera Corporation/Applied Biosystems Group 1999 Stock
                  Incentive Plan, as amended October 17, 2002 (incorporated by
                  reference to Appendix B to Schedule 14A, filed September 6,
                  2002, containing the Company's definitive Proxy Statement for
                  its 2002 Annual Meeting of Stockholders (Commission file
                  number 1-4389)).

Exhibit 23.1      Consent of PricewaterhouseCoopers LLP.

Exhibit 23.2      Consent of Thomas P. Livingston, Esq. (included in Exhibit 5).

Exhibit 24        Power of Attorney (contained on the signature pages hereof).

                                       3
SIGNATURES

      Pursuant to the requirements of the Securities Act of 1933, the Company
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Norwalk, State of Connecticut, on December 13, 2002.

                                        APPLERA CORPORATION

                                        By: /s/ William B. Sawch
                                            ------------------------------------
                                            William B. Sawch
                                            Senior Vice President and
                                            General Counsel

                                POWER OF ATTORNEY

      We, the undersigned directors and officers of the Company, do hereby
constitute and appoint Dennis L. Winger and William B. Sawch, or either of them,
our true and lawful attorneys and agents, to do any and all acts and things in
our name and on our behalf in our capacities as directors and officers and to
execute any and all instruments for us and in our names in the capacities
indicated below, which said attorneys and agents, or either of them, may deem
necessary or advisable to enable said corporation to comply with the Securities
Act of 1933 and any rules, regulations and requirements of the Securities and
Exchange Commission, in connection with this Registration Statement, including
specifically, but without limitation, power and authority to sign for us or any
of us in our names in the capacities indicated below, any and all amendments
(including post-effective amendments) hereto and we do hereby ratify and confirm
all that said attorneys and agents, or either of them, shall do or cause to be
done by virtue hereof.

      Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.
/s/ Tony L. White                     Chairman of the Board,              December 13, 2002
------------------------------------        President and
Tony L. White                               Chief Executive Officer
                                            (Principal Executive Officer)
4
/s/ Dennis L. Winger                  Senior Vice President and           December 13, 2002
------------------------------------        Chief Financial Officer
Dennis L. Winger                            (Principal Financial Officer)

      /s/ Vikram Jog                        Controller                          December 13, 2002
------------------------------------        (Principal Accounting Officer)
Vikram Jog

      /s/ Richard H. Ayers                   Director                           December 13, 2002
------------------------------------
Richard H. Ayers

      /s/ Jean-Luc Belingard                 Director                           December 13, 2002
------------------------------------
Jean-Luc Belingard

      /s/ Robert H. Hayes                    Director                           December 13, 2002
------------------------------------
Robert H. Hayes

      /s/ Arnold J. Levine                   Director                           December 13, 2002
------------------------------------
Arnold J. Levine

      /s/ Theodore E. Martin                 Director                           December 13, 2002
------------------------------------
Theodore E. Martin

      /s/ Carolyn W. Slayman                 Director                           December 13, 2002
------------------------------------
Carolyn W. Slayman

      /s/ Orin R. Smith                      Director                           December 13, 2002
------------------------------------
Orin R. Smith

      /s/ Georges C. St. Laurent, Jr.        Director                           December 13, 2002
-------------------------------------
Georges C. St. Laurent, Jr.

      /s/ James R. Tobin                     Director                           December 13, 2002
-------------------------------------
James R. Tobin
5
EXHIBIT INDEX

Exhibit No.                        Description
-----------                        -----------

Exhibit 5         Opinion of Thomas P. Livingston, Esq. (including consent).

Exhibit 23.1      Consent of PricewaterhouseCoopers LLP.

Exhibit 23.2      Consent of Thomas P. Livingston, Esq. (included in Exhibit 5).

Exhibit 24        Power of Attorney (contained on the signature pages hereof).

                              6