My husband works in Detroit but we live in Ann Arbor. Detroit city taxes do come out of his paycheck. Do we need to file a separate form for him?

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Yes. You will need to file Detroit City Taxes as a nonresident for his income earned in the city.

He needs Form 5119, City of Detroit NonResident Income Tax Return. See the link for more details: 2019 City of Detroit NonResident Income Tax Return Instructions.

Early on in the Michigan interview, you will be asked if you need a Detroit return. Check the boxes as indicated in the screenshot below: That the taxpayer needs a Detroit City Return and is filing as a Detroit Nonresident.