Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		9 Months Ended
	Mar. 31, 2014	Mar. 31, 2013	Mar. 31, 2014	Mar. 31, 2013
Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported [Line Items]
Income tax benefit (expense)	$ (1,331)	$ 504	$ (4,871)	$ (2,602)
Net income attributable to Zygo Corporation	1,898	980	8,107	3,597
Basic Earnings per Share	$ 0.10	$ 0.05	$ 0.43	$ 0.20
Diluted Earnings Per Share	$ 0.10	$ 0.05	$ 0.42	$ 0.19
Scenario, Previously Reported [Member]
Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported [Line Items]
Income tax benefit (expense)		890		(866)
Net income attributable to Zygo Corporation		1,366		5,333
Basic Earnings per Share		$ 0.07		$ 0.29
Diluted Earnings Per Share		$ 0.07		$ 0.28
Restatement Adjustment [Member]
Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported [Line Items]
Income tax benefit (expense)		504		(2,602)
Net income attributable to Zygo Corporation		$ 980		$ 3,597
Basic Earnings per Share		$ 0.05		$ 0.20
Diluted Earnings Per Share		$ 0.05		$ 0.19