The three IS branches were declared "specially designated global terrorists," a category that imposes sanctions and penalties on foreign persons who pose a serious risk of committing acts of terrorism that threaten US nationals or national security, the State Department said.
The IS group in Libya also was named as a "foreign terrorist organization."
The designations freeze any US assets the groups may have and make it illegal for any American national to knowingly provide those groups or conspire to provide them with material support or resources.
The State Department said the three groups emerged as IS branches in November 2014 when IS leader Abu Bakr al-Baghdadi announced he had accepted oaths of allegiance from fighters in Libya, Yemen and Saudi Arabia.
It said that while IS's presence in each country "is limited to specific geographic locations," the group's affiliates in all three countries had carried out numerous deadly attacks.
The militant group's Yemen branch claimed responsibility for suicide bombings in March 2015 against two mosques in Sanaa, killing more than 120 people.
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The IS affiliate in Saudi Arabia attacked Shia mosques both there and in Kuwait, killing more than 50.
And the group's Libyan affiliate is blamed for kidnapping and executing 21 Egyptian Coptic Christians, as well as killing scores of others.
Separately, the Treasury Department announced sanctions against six men it accused of providing financial support to terrorist groups.
It said the move was aimed at disrupting the fundraising and support networks of Al-Qaeda, Al-Nusra Front, Al-Qaeda in the Arabian Peninsula (AQAP) and the Islamic State group.
The sanctions target "financiers and facilitators responsible for moving money, weapons and people on behalf of these terrorist organizations," said Adam Szubin, the Treasury's acting under secretary for terrorism and financial intelligence.
As one example, Treasury said that Nayif Salih Salim al-Qaysi had been an AQAP "facilitator" who had not only distributed money and weapons to AQAP fighters and allied Yemeni tribal forces, but had helped plan militant operations in Yemen.
Treasury also sanctioned a man in Libya who it said provided substantial support for the Islamic State group's affiliate in the Sinai Peninsula. He was accused of moving hundreds of thousands of dollars, as well as weapons and ammunition, from Libya to the Sinai.