<PAGE>

                                                                    EXHIBIT 99.1

PHOTON DYNAMICS, INC.
CERTIFICATION PURSUANT TO
18 U.S.C. SECTION 1350,
AS ADOPTED PURSUANT TO
SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002*

In connection with the Quarterly Report of Photon Dynamics, Inc. (the "Company")
on Form 10-Q for the quarter ended March 31, 2003, as filed with the Securities
and Exchange Commission on the date hereof (the "Report"), I, Elwood H.
Spedden, President, Chief Executive Officer and Director of the Company,
certify, to the best of my knowledge, pursuant to 18 U.S.C. Section 1350, as
adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that:

     (1) The Report fully complies with the requirements of Section 13(a) or
15(d) of the Securities Exchange Act of 1934; and

     (2) The information contained in the Report fairly presents, in all
material respects, the financial condition of the Company at the end of the
period covered by the Report and results of operations of the Company for the
period covered by the Report.

Dated: May 9, 2003

/s/ ELWOOD H. SPEDDEN
---------------------
Elwood H. Spedden
President, Chief Executive Officer and Director

A signed original of this written statement required by Section 906 has been
provided to Photon Dynamics, Inc. and will be retained by Photon Dynamics, Inc.
and furnished to the Securities and Exchange Commission ("SEC") or its staff
upon request.

* This certification accompanies the Form 10-Q to which it relates, is not
deemed filed with the SEC and is not to be incorporated by reference into any
filing of the Company under the Securities Act of 1933, as amended, or the
Securities Exchange Act of 1934, as amended (whether made before or after the
date of the Form 10-Q), irrespective of any general incorporation language
contained in such filing.

<PAGE>

PHOTON DYNAMICS, INC.
CERTIFICATION PURSUANT TO
18 U.S.C. SECTION 1350,
AS ADOPTED PURSUANT TO
SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002*

In connection with the Quarterly Report of Photon Dynamics, Inc. (the "Company")
on Form 10-Q for the quarter ended March 31, 2003, as filed with the Securities
and Exchange Commission on the date hereof (the "Report"), I, Richard L. Dissly,
Chief Financial Officer and Secretary of the Company, certify, to the best of my
knowledge, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section
906 of the Sarbanes-Oxley Act of 2002, that:

     (1) The Report fully complies with the requirements of Section 13(a) or
15(d) of the Securities Exchange Act of 1934; and

     (2) The information contained in the Report fairly presents, in all
material respects, the financial condition of the Company at the end of the
period covered by the Report and results of operations of the Company for the
period covered by the Report.

Dated: May 9, 2003

/s/ RICHARD L. DISSLY
---------------------
Richard L. Dissly
Chief Financial Officer and Secretary

A signed original of this written statement required by Section 906 has been
provided to Photon Dynamics, Inc. and will be retained by Photon Dynamics, Inc.
and furnished to the Securities and Exchange Commission ("SEC") or its staff
upon request.

* This certification accompanies the Form 10-Q to which it relates, is not
deemed filed with the SEC and is not to be incorporated by reference into any
filing of the Company under the Securities Act of 1933, as amended, or the
Securities Exchange Act of 1934, as amended (whether made before or after the
date of the Form 10-Q), irrespective of any general incorporation language
contained in such filing.