EXHIBIT 31.1

CERTIFICATION PURSUANT TO RULE 13a-14(a) OR 15d-14(a) OF THE SECURITIES EXCHANGE ACT OF 1934,AS ADOPTED PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, J. Bruce Robinson, certify that:

|1) | I have reviewed this quarterly report on Form 10-Q of Zygo Corporation;                                                                                                                                                                                                                                                                
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|2) | Based on my knowledge, thisreport 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)) and internal control
over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:
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| | 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 report is being
          prepared;
      b)Designed
          such internal control over financial reporting, or caused such internal
          control over financial reporting to be designed under our supervision,
          to provide reasonable assurance regarding the reliability of financial
          reporting and the preparation of financial statements for external
          purposes in accordance with generally accepted accounting principles;
      c)Evaluated
          the effectiveness of the registrants disclosure controls and
          procedures and presented in this report our conclusions about the effectiveness
          of the disclosure controls and procedures, as of the end of the period
          covered by this report based on such evaluation; and
      d)Disclosed
          in this 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
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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):
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| | 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.
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|Date: May 9, 2007 |                                                                          
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|                  | /s/ J. Bruce RobinsonJ. Bruce RobinsonChairman andChief Executive Officer



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