Whether you are legally separated or are living apart informally, you can still prepare a joint return. You can even do it if you've actually filed for divorce, as long as the divorce isn't final as of Dec. 31 of the tax year [source: Bird]. However, just because you can file a joint tax return doesn't mean you should.
Can separated couples file taxes jointly?
Filing status
The IRS considers you married for the entire tax year when you have no separation maintenance decree by the final day of the year. ... You can only choose "married filing jointly" or "married filing separately" status. You cannot file as "single" or "head of household."
What happens if your married but separated?
Separation means that you are living apart from your spouse but are still legally married until you get a judgment of divorce. Although a separation doesn't end your marriage, it does affect the financial responsibilities between you and your spouse before the divorce is final.