Mammals
41 species of endemic mammal are found in the Rift. Many of these are small mammals such as shrews, rats and bats. A few of the larger ones include the Rwenzori duiker (Cephalophus rubidus) which only occurs at high altitudes in the Rwenzori massif and the Golden monkey (Cercopithecus kandti) which is confined to the Virunga Volcanoes. A few larger mammals are near-endemic species, such as L’hoest’s guenon (Cercopithecus l’hoesti). A list of the endemic and near endemic mammals is provided in the table below. The IUCN classification is given (CR=Critically endangered; EN=endangered; VU=vulnerable; DD=data deficient; NT=near threatened). AR=Albertine Rift endemic; NE=near-endemic species.
| Family | Species | Common name | IUCN | AR endemic |
| Bovidae | Cephalophus rubidus | Ruwenzori Duiker | | AR |
| Cercopithecidae | Cercopithecus mitis kandti | Golden monkey | EN | AR |
| Cricetidae | Delanymys brooksi | Delany's Mouse | VU | AR |
| Cricetidae | Dendromus kahuziensis | Kahuzi Climbing Mouse | CR | AR |
| Cricetidae | Dendromus kivu | Rwenzori/Kivu Climbing mouse | | AR |
| Hominidae | Gorilla beringei | Mountain and Grauers gorilla | CR | AR |
| Muridae | Dasymys montanus | Montane Marsh Rat | EN | AR |
| Muridae | Grammomys dryas | Montane Thicket Rat | NT | AR |
| Muridae | Lophuromys cinereus | | DD | AR |
| Muridae | Lophuromys medicaudatus | | VU | AR |
| Muridae | Lophuromys rahmi | | EN | AR |
| Muridae | Lophuromys woosnami | Woosnam's Brush-furred rat | | AR |
| Muridae | Mus bufo | Western Rift Pygmy Mouse | | AR |
| Muridae | Praomys degraafi | | | AR |
| Muridae | Praomys montis | | | AR |
| Muridae | Thamnomys kempi | Kemp's Thicket Rat | VU | AR |
| Muridae | Thamnomys venustus | Charming Thicket Rat | VU | AR |
| Rhinolophidae | Rhinolophus hillii | Hill's Horseshoe Bat | CR | AR |
| Rhinolophidae | Rhinolophus ruwenzorii | Ruwenzori Horseshoe Bat | VU | AR |
| Rhinolophidae | Rhinolophus willardi | Willard's Horseshoe Bat | | AR |
| Rhinolophidae | Rhinolophus kahuzi | Kahuzi horeshoe bat | | AR |
| Rhizomyidae | Tachyoryctes ruandae | Mole rat/Desmol | | AR |
| Sciuridae | Funisciurus carruthersi | Carruther's Mountain Tree Squirrel | | AR |
| Sciuridae | Heliosciurus ruwenzorii | Montane Sun Squirrel | | AR |
| Soricidae | Crocidura kivuana | Kivu Shrew | VU | AR |
| Soricidae | Crocidura lanosa | Kivu Long-haired Shrew | EN | AR |
| Soricidae | Crocidura lwiroensis | Kabogo Crocidura | | AR |
| Soricidae | Crocidura niobe | Ruwenzori Musk Shrew | NT | AR |
| Soricidae | Crocidura stenocephala | Musk Shrew | EN | AR |
| Soricidae | Myosorex babaulti | Mouse Shrew | NT | AR |
| Soricidae | Myosorex blarina | Ruwenzori Mouse Shrew | EN | AR |
| Soricidae | Myosorex bururiensis | Bururi Forest Shrew | | AR |
| Soricidae | Myosorex jejei | Kahuzi Swamp Shrew | | AR |
| Soricidae | Myosorex kabogoensis | Kabogo Myosorex | | AR |
| Soricidae | Myosorex schalleri | Schaller's Mouse Shrew | DD | AR |
| Soricidae | Paracrocidura graueri | Grauer's Montane Shrew | DD | AR |
| Soricidae | Paracrocidura maxima | East African Montane Shrew | NT | AR |
| Soricidae | Ruwenzorisorex suncoides | Osgood's Montane Shrew | VU | AR |
| Soricidae | Sylvisorex lunaris | | VU | AR |
| Soricidae | Sylvisorex vulcanorum | | NT | AR |
| Tenrecidae | Micropotamogale ruwenzorii | Ruwenzori Otter Shrew | NT | AR |
| Cercopithecidae | Cercopithecus hamlyni | Owl-faced monkey | VU | NE |
| Cercopithecidae | Cercopithecus lhoesti | L'hoest's monkey | VU | NE |
| Cercopithecidae | Lophocebus ugandae | Uganda mangabey | | NE |
| Galagonidae | Galago matschiei | Spectacled Galago | | NE |
| Viverridae | Genetta victoriae | Giant Forest Genet | | NE |
| Viverridae | Osbornicitis piscivora | Aquatic Genet | DD | NE |
| Soricidae | Crocidura maurisca | Northern Swamp Musk Shrew | | NE |
| Soricidae | Crocidura montis | Eastern Montane Musk Shrew | | NE |
| Soricidae | Scutisorex somereni | Hero Shrew | | NE |
| Soricidae | Sylvisorex granti | Least Long-tailed Forest Shrew | | NE |
| Rhizomyidae | Tachyoryctes ankoliae | Mole rat/Desmol | VU | NE |
| Muridae | Hybomys lunaris | Ruwenzori Striped Mouse | VU | NE |