You can still file as Married Filing Joint even if you are living separately (& even if only one spouse has income), you both must agree to file Jointly. You enter the address on your tax return that you would want the IRS or State to contact you if they needed to. The program will also ask if either of you lived in a different state. You both would have to file separate State returns, depending on your State's filing requirements.
Also, when married & living apart you can also file as Married Filing Separate (each file their own tax return & enter their own information), or Head of Household, if you quality.
You can file your Federal return jointly, even though you live in separate states, and you can list your current addresses in the MY INFO section for each of you.
If either of you moved during the year, you may need to file Part-Year Resident Returns to both states you lived and had income in.
If not, you can each file a Separate Resident State return to the state you lived in all year.
Click the link for detailed instructions on How to File Joint Federal and Separate State Returns.
You can still file as Married Filing Joint even if you are living separately (& even if only one spouse has income), you both must agree to file Jointly. You enter the address on your tax return that you would want the IRS or State to contact you if they needed to. The program will also ask if either of you lived in a different state. You both would have to file separate State returns, depending on your State's filing requirements.
Also, when married & living apart you can also file as Married Filing Separate (each file their own tax return & enter their own information), or Head of Household, if you quality.