You always have the option to file a joint return no matter where he is ... or file separately ... or if you have a qualifying person you can claim Head of Household. You need to consider all the options and pick one that suits you best.
Do you have children you support? If so, you may be able to file as Head of Household if you and your dependents meet the criteria.
If not, then filing as Married Filing Separate is what most people choose when they are a US Citizen married to someone, not in this country. You will still need to print and write NRA in the spouses section of your return then mail your return as you would need your spouse's SSN to e-file your return.
There is the option of Married Filing Jointly, however, you would need to apply for an ITIN for your spouse and include all income he earned worldwide. https://www.irs.gov/individuals/international-taxpayers/nonresident-alien-spouse