Hi, I was a F1 student in US since Aug.2003 to Sept.2007. For these years I consider myself as a nonresident alien for tax purpose.

Then I graduated and got H1B in Oct.1 2007. And since then on, I consider myself as a resident alien for tax purpose.

In Sept.2008 I married a US citizen. In Dec. 2008 we filed green card application, but didn't get approved until 2009.

My question is, in the tax return for 2008, I read that I could claim the tax treaty, as I came with F1 and later converted to H1B. Does the marriage make me unable to claim it? What if I file "married and file separately?"

Thanks!

For 2008 you must file resident tax return. You can only file as married filing jointly or married filing separately.
You will not get treaty deduction on H1-B visa.
Read about F1/H1-B tax filing: Your U.S. Tax Return: The U.S. Visas (http://taxipay.blogspot.com/2008/08/us-visas.html)

What country are you from?

I was born in China.

I read from other threads, that there's some clause that makes me eligible to claim tax treaty even under H-1B as long as I entered US with F1 visa.

IRS publication 678 FS provides:

A student from China is entitled to the $5,000 exemption for the amount of time reasonably necessary to complete education or training. A student will become a resident alien for tax purposes after 5 years but is still entitled to the treaty benefit as long as he or she remains a student.

After you changed to H!B, you were no longer a student.

I agree with IntlTax, but I believe that you CAN claim the $5,000treaty exemption in the year you switched to H-1B if you spent more than six months on F-1 status in that year.