Last year my friend had filed MFJ for 2008. He got married on Dec 22nd 2008. His wife came to US in Jan 2009 and they filed MFJ.He
Attached a statement with his return declaring that one spouse is a non resident alien and the other spouse a US resident and that they choose to be US residents for the entire tax year.

In July 2009, his wife separated from him and went back to India. This Jan 2010 they filed for divorce.

What Filing status should he use for 2009? Is it MFS or Single? Is there any implications for declaring themselves as residents in the 2008 return (Pub 519)

Thanks in advance,

He can file as married filing jointly or married filing separately. He can not file as single.

Can he file MFJ, even if they lived apart from July? Then how do he get her to sign the return? If he e- files, should she not sign Form 8879.

Yes, they can file joint return. On the joint return, both must sign.