EXHIBIT 31.1

Certifications:
Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

I, J. Bruce
Robinson, certify that:

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

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;

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;

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)) 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

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):

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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.                                                                                                 

|                    |                                                                          | 
|------------------- | ------------------------------------------------------------------------ | 
|Date: July 20, 2006 |                                                                         
|                    |                                                                         
|                    | /s/ J. Bruce
  Robinson                                                  | 
|                    |                                                                          | 
|                    | J. Bruce
  Robinson
  Chairman, President, and
  Chief Executive Officer

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