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                                                                    EXHIBIT 31.1

                           CERTIFICATION OF DISCLOSURE
                        IN THE REGISTRANT'S ANNUAL REPORT

I, J. Bruce Robinson, certify that:

1) I have reviewed this annual report on Form 10-K of Zygo Corporation;

2) Based on my knowledge, this annual 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 annual
report;

3) Based on my knowledge, the financial statements, and other financial
information included in this annual 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 annual report;

4) The registrant's other certifying officer 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:

     a) designed such disclosure controls and procedures, or caused such
     disclosure controls and procedures to be designed under our supervision, to
     ensure that material information relating to the registrant, including its
     consolidated subsidiaries, is made known to us by others within those
     entities, particularly during the period in which this annual report is
     being prepared;

     b) evaluated the effectiveness of the registrant's disclosure controls and
     procedures and presented in this annual report our conclusions about the
     effectiveness of the disclosure controls and procedures, as of the end of
     the period covered by this annual report based on such evaluation; and

     c) disclosed in this annual report any change in the registrant's internal
     control over financial reporting that occurred during the registrant's most
     recent fiscal quarter (the registrant's fourth fiscal quarter in the case
     of an annual report) that has materially affected, or is reasonably likely
     to materially affect, the registrant's internal control over financial
     reporting; and

5) The registrant's other certifying officer 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 registrant's board of directors
(or persons performing the equivalent functions):

     a) all significant deficiencies and material weaknesses in the design or
     operation of internal control over financial reporting which are reasonably
     likely to adversely affect the registrant's ability to record, process,
     summarize and report financial information; and

     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.

Date: September 13, 2004


                                        /s/ J. Bruce Robinson
                                        ----------------------------------------
                                        J. Bruce Robinson
                                        Chairman, President, and
                                        Chief Executive Officer