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If you were a member of the military during the taxable year and your domicile is California, they consider you a resident of California. While stationed in California on permanent military orders, you are subject to tax on all income regardless of its source. While stationed outside of California on Permanent Change of Station (PCS) Orders, you are not subject to tax on your military wages.
Since the California tax return starts with Federal AGI, you must make an adjustment on your CA return. You will file as a Nonresident of California. Here is alink to the CA Publication 1032 that is geared toward military personnelhttp://www.ftb.ca.gov/forms/2010/10_1032.pdf