Employee Tax Expert
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Tax help for military filers

Illinois is taxing her income as well.  You will want to file Kansas as a nonresident then she will get the withholding back and then you can use it to pay the IL tax.  If she qualifies as IL resident, you want to keep it or she will have to stay as KS resident if you PCS.  She can also ask her employer for the form so that KS tax is not taken out so you do not have to file two returns next year.