EXHIBIT 31.2

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,
      Walter A. Shephard, 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/ Walter A. Shephard                
|                         | Walter A. Shephard                    
|                         | Vice President, Finance,              
|                         | Chief Financial Officer, and Treasurer

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