EXHIBIT 31.1

CERTIFICATION PURSUANT TO RULE 13a-14(a) OR 15d-14(a) OF THE SECURITIES EXCHANGE ACT OF1934, AS ADOPTED PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

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|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;                                                                                         
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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.                                                                                                                                                                                                             
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|Date:
      September 19, 2007     

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

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