The Cape Region lacks a distinctive mammal fauna. This region contains 127 species of native mammals, with 90 being present in the Southwest Cape area. The regional total is less than half of the mammal species occurring within all of South Africa. The largest orders present are the Rodentia and the Carnivora.
The rodents are represented by two species of mole rats (Bathyergidae), a porcupine (Hystricidae), two dormice (Muscardinidae), and at least 21 species of Muridae and Cricetidae. There are 27 species of the Carnivora, ranging from mustelids and civets to larger hyenas, jackals, and cats.
Large browsers and grazers play an important role in this ecosystem in comparison with other MTEs. There are 20 species of Artiodactyla and five species of Perissodactyla. Very few of these depend on grazing, however, because of the paucity and poor nutritive value of Cape Region grasses. The Chiroptera is a large group with one fruit bat and 14 species of Microchiroptera in the Southwest Cape.
The abundance and diversity of native mammals was probably always relatively low in fynbos shrublands, unlike the rich savanna regions of the continent. At the time of European colonization the highest numbers and diversity of large mammals was present in renosterveld or other open communities with better browse. Large mammals that were once common on the renosterveld plains included bontebok, eland, buffalo, Cape mountain zebra, red hartebeest, and lion.
Endemism, as might be expected, is quite low among mammals in the Cape Floristic Region as most of this fauna extends northward or westward into arid or savanna ecosystems. Only four species in the mammal fauna are endemic. The fossorial Cape dune mole rat and burrowing gerbil among the endemic rodents are associated with sandy soil substrates rather than with any specific vegetation type. The colonial behavior and feeding specialization of mole rats on bulbs may be linked to the remarkably high diversity of geophytes in the Cape Floristic Region.
The regularly occurring bird fauna includes 324 species, with a notable diversity of Falconiiformes with 22 species. Six bird species are endemic. Endemic species are largely dietary specialists such as the Cape sugarbird, orange-breasted sunbird, and Protea seedeater that are tied to specific plant resources in the fynbos. The originally direct communication of fynbos habitats with semiarid and savanna shrublands has probably been a factor in limiting the number of endemic fynbos birds. The savanna region of South Africa is far richer in endemic species. At least four of the endemic fynbos birds are characteristic of montane areas or are allied to montane species of East Africa that live in ericaceous shrublands. For fynbos communities specifically, there are only about 10 reported species, with renosterveld habitats generally richer at a local level.
The Cape Region is moderately diverse in reptiles with 100 species present, 22 of which are endemic. Fynbos communities may contain more than 50 species of lizards. The Gekkonidae are the most important group with 18 species. There are 32 species of snakes reported from the Western Cape area. Among snakes, the Colubridae have the highest diversity with 25 species. There are 19 endemic species among the reptiles, 17% of the total. One notable endemic to the southwestern Cape Region is Psammobates geometricus, one of the rarest tortoises in the world. The life history of this species seems to have evolved to adapt to fynbos fire cycles, with hatchlings appearing in late autumn after the danger of summer fires is past.
Amphibians are relatively low in diversity in the Cape Region with 51 native species, 16 of these endemic. The largest single group of amphibians is the Ranidae with 13 species. One of the most interesting endemics among amphibians is the arum lily frog, Hyperolius horstocki, which lives in the flowers of the common arum lily (Zantedeschia aethiopica).
There are 34 native fish species in the Cape Region, 14 of these being endemic.