The employer filed the Social Security and Medicare taxes with the Social Security Administration so you will get full credit for those for the year. You will have to file a Puerto Rico tax return to report the income and pay the taxes (just like in the U.S.)- it should be a simple return as it will only include the Puerto Rico income. You will have to report all of the income on your U.S. tax return, but claim the credit for the taxes paid to Puerto Rico. @mythicpilot
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