I am a US citizen. I married last June 2008. My wife originally entered US on a J-1 Visa as a scholar in 2007 and filed taxes as nonresident for that year (NR1040). So for 2007 and 2008 no FICA taxes were deducted from her pay check. Now 2009 she is paying FICA. If we file a joint return for 2008 are we liable for FICA for 2008?

Thank you for your help!

Yes, you can file joint return as residents. Then she must start paying FICA taxes from 2009. If she did not pay FICA taxes for 2008, then there is no way she can pay it herself.

She is NOT liable for FICA for 2008, even if you filed jointly.