If you are legally married and you have not lived apart from one-another for the last 6 months of 2016, you only have the option of filing Married Filing Jointly (MFJ) or Married Filing Separately (MFS).
Usually you are better to file Married Filing Jointly because you get to claim his exemption and you get a higher Standard Deduction.
There may also be credits you could be eligible for that you would lose filing Married Filing Separately.