Characteristic species are the "big five", spotted hyena, impala, nyala, majestically horned kudu, white bushbuck, sable antelope, zebra, giraffe and wildebeest. Rhino, elephant and buffalo are frequently sighted. Sightings of civet and genet cats, porcupine and honey badger have also been noted.
The granite hilltops and boulder outcrops at Bongani provide an important habitat for a number of plant and animal species that are not found or are rare on the wooded slopes and valleys. The agile, solidly built klipspringers are confined to rocky places and the socially complex chacma baboons use the highest peaks as lookout points.
Predators include lion and leopard. Critically endangered wild dog can be seen in the Mthethomusha Game Reserve as well as in the adjoining Kruger National Park.
In the region of 320 species of birds inhabit the reserve. One of the most conspicuous birds to be seen on the rocks around Bongani Lodge is the lively Mocking Chat. Of the many species of birds of prey, none is more frequently seen than the loudly wailing Jackal Buzzard.
Typical birds include Red-winged Starling, Familiar Chat, Rock Bunting, Black Sunbird, Purple-crested Lourie, Golden-breasted Bunting, Black-eyed Bulbul and Freckled Nightjar. There are also Crowned Eagles, Bateleur and several species of vulture.
The craggy rocks of the area provide an ideal environment for numerous species of lizards, including the Common Flat Lizard, Giant Plated Lizard, Rainbow Skink, Striped Skink and Common Dwarf Gecko on rocks near the lodge. Crocodile are common in the adjoining Kruger National Park.
Hardy plants of rocky habitats include Kudu Lily, Baboon's Tail/Fire Sticks, Barberton Daisy, Rock Aloe and Lebombo Aloe. The most unusual tree growing among the rocks at Bongani is the scarlet-blooming Broadleaved Coral Tree, whose three leaflets are each about the size of an outstretched human hand. Other exquisite trees around Bongani include Lowveld Chestnut, rock-breaking Mountain Fig, Mountain Syringa, Mountain Karee, Common Cabbage Tree, Jacketplum and Wild Pear.