If you are separated or have filed for divorce you can still file your taxes jointly with your spouse so long as you are not legally divorced. If you divorced at some point during the year you will be unable to file jointly.  

While you may be angry or upset with your soon-to-be ex-spouse it might be financially beneficial to file taxes married filing jointly. If you choose not to file jointly and separate in the middle of the year you will have to address who will elect the children as dependents and who will claim the interest on your mortgage. If you pay childcare expenses you will want to allocate those expenses appropriately. These are issues you will have to resolve if you intend to file married filing separately or whether you are eligible to claim head of household.  

The tax issue may become more complicated when one party is self-employed and pays estimated taxes or has not paid enough estimated taxes and therefore you have to determine who is responsible for taxes owed. If you file separately you may still be obligated to contribute to the taxes owed by your spouse if you benefited from the income they received that year.  

If you are concerned that your spouse has unreported income or has inaccurately accounted for business expenses, you can have your spouse sign an indemnification agreement whereby your spouse would agree to pay any taxes, interest, and penalties owed if the IRS later determines that he or she has not accurately reported income. While the IRS can still seek payment from you if you file a joint return, you will be able to enforce the indemnification agreement in family court and require your spouse to be responsible for all taxes owed.  

There are many considerations that you should explore with your family lawyer regarding tax filing when you are in the middle of a divorce but ultimately it is best to seek the advice of an accountant as to the preferable filing status as well.