The Allied Democratic Forces (ADF) in Congo and its leader Seka Musa Baluku and Mozambique's Ahlu Sunnah Wa-Jama and its leader Abu Yasir Hassan were also named "specially designated global terrorists."
The designations prevent travel by members to the United States, freeze any U.S.-related assets, ban Americans from doing business with them and make it a crime to provide support or resources to the movements.
The United States dubbed the groups ISIS-DRC and ISIS-Mozambique.
"The Islamic State of Iraq and Syria (ISIS) announced the launch of the Islamic State Central Africa Province (ISCAP) in April 2019 to promote the presence of ISIS associated elements within Central, East, and Southern Africa," the State Department said in a statement.
"Although ISIS-associated media portray ISCAP as a unified structure, ISIS-DRC and ISIS-Mozambique are distinct groups with distinct origins," it said. "These groups have committed or pose a significant risk of committing acts of terrorism."
The Allied Democratic Forces (ADF), a Ugandan insurgent faction active in eastern Congo since the 1990s, has committed a spate of brutal reprisal attacks on civilians since the army began operations against it in late 2019.
The ADF has been blamed for the killing of over 140 people since the start of the year, in almost weekly attacks in Congo’s restive east. The group killed around 850 people last year, according to U.N. figures.
Islamic State funding and recognition has driven the ADF into a new phase of deadly expansion, said Laren Poole from the Bridgeway Foundation, a U.S. based thinktank.
"We believe that targeting the group's financial and recruitment networks will provide the most effective way to reduce the Islamic State in DRC's capacity for violence," Poole told Reuters.
Some analysts, though, have questioned links between the ADF and Islamic State.
"These new sanctions probably won't have much effect on the ground, just as the sanctions on ADF in 2014 changed nothing," said Dan Fahey, a former member of an independent group of experts charged with monitoring U.N. sanctions on DRC.
"It is a symbolic act, and a bit surprising because the group of experts has consistently downplayed the nature and strength of the ISIS influence in Congo," he added.Ahlu Sunnah Wa-Jama, known in Mozambique as Al-Shabaab, staged its first attack in 2017. First known mainly for beheadings, the fighters declared allegiance to Islamic State in 2019 and have since increased attacks in scale and frequency.