The Park supports a variety of wildlife including rock and tree hyraxes, elephant, buffalo, Defassa waterbuck, oribi, bushbuck, duiker, forest hog, bush pig, leopard, civet and serval cats, serval cats, spotted hyena; aardvark and several rodent species. However these animals are rarely observed in the forest setting. More commonly seen creatures are the black-and-white colobus; baboons; red tailed, vervet, De Brazza’s and blue monkeys; duiker and tree squirrel.
The mountain is home to 300 birds including 40 restricted range species. 56 of the 87 Afrotropical highland biome species live here, notably the Moorland Francolin, Moustached Green Tinkerbird and Alpine Chat.
Birds whose Ugandan range is limited to Mount Elgon include the Jackson's Francolin and Black-collared Apalis. Among those limited to just a few mountains in eastern Uganda are the Black-shouldered Kite and Tacazze Sunbird. Mount Elgon is one of the few places in Uganda where the endangered Lammergeyer can be seen, soaring above the caldera and Suam Gorge.
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