I was on opt for year 2007. Since 2008 I have been paying FICA and other taxes. In January 08 I was paid annual bonus for year 2007. My question is, do I pay fica on this bonus even though it was for yea 2007 in which is was exempt since this bonus was credited in jan 2008.

The bonus received in 2008 is income for the year 2008. If you are on H1-B, then it will be subject to FICA taxes.
Also, if the employer did not deduct FICA taxes, then it will be reported on 1099-misc. This is income as independent contractor and is reported on schedule C or C-EZ (Form 1040). Net income is subject to SE tax at 15.3%.
How you will treat the 1099-Misc income, read: Your U.S. Tax Return: W2 vs 1099-Misc: Employee vs Independent Contractor.

The fact that you were on OPT would lead me to believe that you were under a F-1 visa.

If this was the case, and assuming your F-1 visa was issued in 2003 or later, then you are NOT LIABLE for FICA taxes for 2007.

If your F1 visa was issued in 2004 or later, then you are NOT LIABLE for FICA taxes for 2008 as well.

If these are the facts, you may need to submit For 843 to request a refund of these taxes from the IRS. Email me at the address below for details on how to proceed.