You can choose between the married filing joint, married filing separate, and (depending on how much of the year he was incarcerated) head of household filing status.
There are a couple of issues if you file as married filing joint:
He may have taxable income in prison. You will need to include that income on your return.
Prison wages are not considered earned income for the earned income credit.
The lack of earned income from your spouse will prevent you from taking the child care credit.
If he was incarcerated for more than the last 6 months of 2016 and you have children that live with you and are your dependents, you can be considered unmarried in order to claim head of household filing status. See the following rules for being considered unmarried from IRS Pub 501:
You file a separate return. A separate return includes a return claiming married filing separately, single, or head of household filing status.
You paid more than half the cost of keeping up your home for the tax year.
Your spouse didn't live in your home during the last 6 months of the tax year. Your spouse is considered to live in your home even if he or she is temporarily absent due to special circumstances. See Temporary absences , later.
Your home was the main home of your child, stepchild, or foster child for more than half the year. (See Home of qualifying person , later, for rules applying to a child's birth, death, or temporary absence during the year.)
You must be able to claim an exemption for the child. However, you meet this test if you can't claim the exemption only because the noncustodial parent can claim the child using the rules described later in Children of divorced or separated parents (or parents who live apart) under Qualifying Child or in Support Test for Children of Divorced or Separated Parents (or Parents Who Live Apart) under Qualifying Relative. The general rules for claiming an exemption for a dependent are explained later under Exemptions for Dependents .
Head of Household filing status will allow you to avoid the issues mentioned above.
