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Recommend you review Tax Topic 901 which specifies US govt employees in Puerto Rico must include their wages on a US tax return. Quote from TT901:
"However, if you are a bona fide resident of Puerto Rico and a U.S. government employee, you must file a U.S. income tax return reporting all income received for performing services for the U.S. government, including services performed in Puerto Rico as a U.S. government employee. If you are a member of the U.S. Armed Forces or a civilian spouse of an active duty member of the U.S. Armed Forces, special income tax filing rules may apply to you. For more information, please refer to Publication 570 and Notice 2012-41."
However, Pub 570, Chapter 3 indicates he needs to file a Puerto Rico tax return in addition, pay taxes, then obtain a foreign tax credit on his US1040 for taxes paid to Puerto Rico. From Pub 570:
"U.S. Government employees. Wages and cost-of-living allowances paid by the U.S. Government (or one of its agencies) for working in Puerto Rico are subject to Puerto Rico tax. However, the cost-of-living allowances are excluded from Puerto Rico gross income up to the amount exempt from U.S. tax. In order to claim this exclusion, you must:
Include with your Puerto Rico tax return evidence to show the amount received during the year, and
Be in full compliance with your Puerto Rico tax responsibilities.
See:
https://www.irs.gov/taxtopics/tc901.html
https://www.irs.gov/publications/p570/ch03.html#en_US_2014_publink1000221281
Recommend you review Tax Topic 901 which specifies US govt employees in Puerto Rico must include their wages on a US tax return. Quote from TT901:
"However, if you are a bona fide resident of Puerto Rico and a U.S. government employee, you must file a U.S. income tax return reporting all income received for performing services for the U.S. government, including services performed in Puerto Rico as a U.S. government employee. If you are a member of the U.S. Armed Forces or a civilian spouse of an active duty member of the U.S. Armed Forces, special income tax filing rules may apply to you. For more information, please refer to Publication 570 and Notice 2012-41."
However, Pub 570, Chapter 3 indicates he needs to file a Puerto Rico tax return in addition, pay taxes, then obtain a foreign tax credit on his US1040 for taxes paid to Puerto Rico. From Pub 570:
"U.S. Government employees. Wages and cost-of-living allowances paid by the U.S. Government (or one of its agencies) for working in Puerto Rico are subject to Puerto Rico tax. However, the cost-of-living allowances are excluded from Puerto Rico gross income up to the amount exempt from U.S. tax. In order to claim this exclusion, you must:
Include with your Puerto Rico tax return evidence to show the amount received during the year, and
Be in full compliance with your Puerto Rico tax responsibilities.
See:
https://www.irs.gov/taxtopics/tc901.html
https://www.irs.gov/publications/p570/ch03.html#en_US_2014_publink1000221281
You will enter this information in a Form 2555 (Foreign Earned Income Exclusion) or Form 2555-EZ is simplified version of this form.
Here's how to add – or remove – a Form 2555 or 2555-EZ from your return:
Tip: The -T or -S suffix after the 2555 stands for taxpayer or spouse, respectively.
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