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If you are not divorced then the only options is Joint, (if you both agree and both sign the return), Married Filing Separately or possibly Head of Household if you have your child, step-child or foster child that lives with you that you can claim as a dependent.
If you were not legally divorced, you would have to file as Married- Joint, Separate or Head of Household (if you qualify). In your case, since you lived apart, you most likely should file Separate. See Tax Tips for Separated Couples - TurboTax Tax Tips & Videos.
even though separated you can still file jointly with your spouse if he consents. however, that could make you liable if he doesn't provide you with all his income unless you file an innocent spouse allocation form (form 8379) with the joint return. if you choose not to file jointly then if you had a qualifying child and paid more than 1/2 the cost of keeping up a home for yourself and the child you can file using the head of household status otherwise you must use the married filing separate status. the MFS requires you to provide his name and social security number on your MFS return and to both of you must use either the itemized or standard deduction. if you can't obtain his SSN you'll have to mail in your return and provide his name and last known address in a statement that says you're filing sperate and can't obtain your spouse's SSN
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