It depends on whether you are legally separated (you have a decree of separate maintenance) or just separated.
The IRS says in this document:
If you're separated but not legally separated or divorced at the end of the year
The IRS considers you married for filing purposes until you get a final decree of divorce or separate maintenance.
In this case, if you don't agree to file jointly, you must file Married filing Separately.
If you're legally separated or divorced at the end of the year
You must file as single for that tax year unless you're eligible to file as head of household or you remarry by the end of the year.
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