Income Taxes (Details) - Schedule of reconciliation of restated balance sheet to previously reported (USD $) In Thousands, unless otherwise specified	Mar. 31, 2014	Jun. 30, 2013
Income Taxes (Details) - Schedule of reconciliation of restated balance sheet to previously reported [Line Items]
Deferred income taxes - Asset - Current	$ 8,214	$ 10,490
Total current assets	180,686	165,003
Total assets	230,542	215,113
Other long term liabilities	4,778	3,769
Total liabilities	34,682	31,108
Retained earnings	34,962	26,855
Total shareholders’ equity - Zygo Corporation	193,948	181,962
Total equity	195,860	184,005
Total liabilities and equity	230,542	215,113
Scenario, Previously Reported [Member]
Income Taxes (Details) - Schedule of reconciliation of restated balance sheet to previously reported [Line Items]
Deferred income taxes - Asset - Current		7,261
Total current assets		163,633
Deferred income taxes - Asset - Long Term		14,967
Total assets		218,220
Other long term liabilities		4,997
Total liabilities		32,336
Additional paid-in capital		180,324
Retained earnings		30,104
Total shareholders’ equity - Zygo Corporation		183,841
Total equity		185,884
Total liabilities and equity		218,220
Restatement Adjustment [Member]
Income Taxes (Details) - Schedule of reconciliation of restated balance sheet to previously reported [Line Items]
Deferred income taxes - Asset - Current		8,631
Total current assets		165,003
Deferred income taxes - Asset - Long Term		10,490
Total assets		215,113
Other long term liabilities		3,769
Total liabilities		31,108
Additional paid-in capital		181,694
Retained earnings		26,855
Total shareholders’ equity - Zygo Corporation		181,962
Total equity		184,005
Total liabilities and equity		$ 215,113