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:

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|1) | I have reviewed this annual report on Form 10-K of
  Zygo Corporation;                                                                                                                                                                                                                                                                         
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|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;                                                  
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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:
|   |                                                                                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                                                                                                                              
|   |                                                                                                                                                                                                                                                                                                                                                 | 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(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):                                     
|   |                                                                                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                                                                                                                              
|   |                                                                                                                                                                                                                                                                                                                                                 | 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 11, 2006

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

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