American Samoa, Guam, the CNMI, the U.S. Virgin Islands, and Puerto Rico has their own independent tax departments. If you have income from one of these U.S. territories, you may have to file a U.S. tax return only, a territory tax return only, or both returns. This generally depends on whether you are considered a resident of one of the U.S. territories. In some cases, you may have to file a U.S. return, but be able to exclude income earned in a territory from U.S. tax.
Filing requirements for specific U.S. possessions are explained in IRS Publication 570 Tax Guide for Individuals With Income From U.S. Possessions.