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If I work 50% of my job in Missouri and 50% of my job in Illinois during the year, how will my pay be taxed by each state?

Your total gross earnings will be taxed by the percentage of time you worked in each state. For example if your total annual salary is $40,000, $20,000 is taxed as Missouri earnings and $20,000 is taxed as Illinois earnings. Your W-2 will display both states and the state taxes withheld.