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 annual report on Form 10-K/A 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;                                                                                                                      
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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;               
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|   | 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;                      
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|   | 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                                                                                                                
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|   | 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                                                                                                                          
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|   | 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: October 27, 2008

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

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