In a statement, the US Department of State said the Allied Democratic Forces (ADF) were also known as "ISIS-DRC" or "Madina at Tauheed Wau Mujahedeen".
The group is "notorious in this region for its brutal violence against Congolese citizens and regional military forces, with attacks killing over 849 civilians in 2020 alone" according to UN figures, it added.
Commanded by Seka Musa Baluku, the ADF has come into the orbit of IS’ so-called "Central Africa Province" since the terror group launched it in 2019.
It is mostly active in the North Kivu and Ituri provinces along the DRC’s border with Rwanda and Uganda.
As well as the ADF, the State Department also labelled a separate militia in Mozambique, known as Ansar al-Sunna or al-Shabaab, as an IS-linked terror group, saying it "reportedly pledged allegiance to (IS) as early as April 2018".
"Since October 2017, ISIS-Mozambique, led by Abu Yasir Hassan, has killed more than 1,300 civilians," it added.
Nevertheless, both organisations are "distinct groups with distinct origins" from IS itself, the State Department said.
The terror designations freeze any property under US jurisdiction linked to the groups or their leaders, bans transactions with them and threatens foreign financial firms with sanctions if they deal with the groups.
The ADF militia are Ugandan Islamic fighters who have made their base in eastern DR Congo since 1995.
They have not launched raids into Uganda for several years.
Since April 2019, IS has claimed some ADF attacks, sometimes with factual errors, while in December last year a UN expert group found "no direct link" between the two.
Blamed for 1,219 civilian killings since 2017, the ADF is believed to be the deadliest of at least 122 armed groups active in DR Congo’s four eastern border provinces of Ituri, North Kivu, South Kivu and Tanganyika.