Your company is required to register in the State of NY as an employer. This sets up withholding and UI tax accounts.New York has such a rule in place, subjecting employees to New York state income taxes if they make the choice to work remotely in another state. This is based on reciprocal agreements between Illinois and these states. When states have reciprocity arrangements with one another, you only need to pay taxes on the related wage income to your state of residence. Yes, you will enter the income that you are reporting as taxable to both states on your New York tax return. Employers are required to withhold and pay personal income taxes on wages, salaries, bonuses, commissions, and other similar income paid to employees. Employers are expected to withhold state income tax from an employee's wages if that employee is subject to state income tax unless noted below. You have to pay taxes in both states and if you pay enough in NY then you don't pay in Illinois. Complete the worksheet on the back of this page to figure the correct number of allowances you are entitled to claim.