If you are legally separated as of the last day of the tax year, then for tax purposes the IRS considers you to be unmarried for the entire year.
Your only choice for filing for 2009 would be single or head of household. You would qualify for HOH if you have a child or other dependent who lives with you and you pay more than half the cost of keeping up the home for that dependent.
You cannot file a joint return and you cannot file as married filing separate returns.
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