To use filing status - married filing jointly - the couple MUST be married at the end of the year. They don't necessarily have to be living together.
IF you are divorced by the end of a tax year - then your correct filing status is Single OR if you have qualifying children - Head of Household
IF married persons are NOT living together they can still file jointly UNLESS they are legally separated. (Meaning there is a decree of divorce or separate maintenance (as of the last day of the year). It gets a little dicey if you are separated under an interlocutory decree of divorce - then your are considered married till it's final.
Basically Legally Separated means you have gone before a judge and you're almost divorced but not quite.
Look at the filing instructions for the F1040 - under filing status.
