Yes, when filing married filing separately both spouses file their own return. Each spouse will list only their spouse's name and social security number on the return.
Married (Filing Separately)
You can be married filing separately if, as of December 31 of the tax year, you:
are married
can provide spouse’s name and social security number on the tax return
This may be an option if you only want to be responsible for your individual tax liability or if you spouse won’t agree to filing a joint tax return.
With this status you only have to report your income. If your spouses itemizes their deductions, you must as well, even if it is lower than the standard deduction.
See link below for more information:
http://blog.turbotax.intuit.com/taxes-101/filing-status-on-taxes-459/