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		6 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2012
Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported [Line Items]
Income tax expense (in Dollars)	$ (2,135)	$ (1,064)	$ (3,540)	$ (3,106)
Net Income attributable to Zygo Corporation (in Dollars)	4,054	838	6,209	2,617
Basic Earnings per Share	$ 0.22	$ 0.05	$ 0.33	$ 0.14
Diluted Earnings Per Share	$ 0.21	$ 0.04	$ 0.32	$ 0.14
Scenario, Previously Reported [Member]
Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported [Line Items]
Income tax expense (in Dollars)		(323)		(1,756)
Net Income attributable to Zygo Corporation (in Dollars)		1,579		3,967
Basic Earnings per Share		$ 0.09		$ 0.22
Diluted Earnings Per Share		$ 0.08		$ 0.21
Restatement Adjustment [Member]
Income Taxes (Details) - Schedule of reconciliation of restated income statement to previously reported [Line Items]
Income tax expense (in Dollars)		(1,064)		(3,106)
Net Income attributable to Zygo Corporation (in Dollars)		$ 838		$ 2,617
Basic Earnings per Share		$ 0.05		$ 0.14
Diluted Earnings Per Share		$ 0.04		$ 0.14