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I was separated from my wife for many years (she was MIA), and have filed "Married filing Separate" for the past 5-6 years. She passed away In may of 2016. Can I file my return as single?
You would file Married Filing Separately in the year of your spouse's death, unless you qualify as Head of Household or Married Filing Jointly (presumably these are not options). Per IRS Publication 501, "If your spouse died during the year, you are considered married for the whole year for filing status purposes."
In 2016, the rules dictating your permitted filing status are essentially unchanged from prior years.
https://www.irs.gov/publications/p501/ar02.html#en_US_2016_publink1000220736
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