You can file married-separate in Illinois so you don't have to file a tax return there.
If you file married-separate, you will need to prepare two federal tax returns, one for your spouse's Illinois return and one joint for federal and California, If you want to file married-joint on your federal tax return. You may find it better to purchase the desktop version of TurboTax if you want to file separate as you can do multiple returns using the same tax product.
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