The Cape Region occupies a small area on the southwestern tip of Africa. This landscape has ancient mountain ranges that have weathered over millions of years into acidic sandy soils that are low in nutrients critical to most plants. The Cape Region is renowned for a showy and diverse flora unlike that of any other area of the world. The characteristic vegetation is fynbos, an evergreen shrubland dominated by the family Proteaceae and a diverse assemblage of small-leaved shrubs. A second important community is renosterveld, a low shrubland which occurs on richer soils. Herbaceous geophytes (i.e. plants with bulbs, tubers, or other fleshy underground organs) are a notable plant group in both communities. Woodland and forest communities are rare.

These formerly high mountains have eroded over the past 200 million years into low ranges capped by resistant Table Mountain sandstone. Separating the mountains are gentle valleys and undulating plains largely underlain by shales with greater nutrient availability. Relatively young Tertiary and Quaternary limestones and sands mantle extensive areas of the coast.

The characteristic vegetation of the Cape Region, particularly on nutrient-poor quartzite soils, is fynbos. Fynbos is an evergreen shrubland dominated by four major plant morphological groups. These include two shrub groups (the proteoids and ericoids), a sedge-like group (restioids), and geophytes. The proteoids, formed by woody Proteaceae, form the tallest matrix of the fynbos community and commonly reach to 2–4 m in height. The ericoid group gains its name from the Ericaceae, but includes more than 3000 species of small-leaved shrubs from many families. The restioids are primarily members of the Restionaceae, a family with origins in Gondwanaland but which diversifiied in fynbos. Finally, the Cape Region contains the highest diversity of bulbs and other geophytes in the world, with more than 1,500 species. Many types of fynbos have been described, but a simple classification scheme includes proteoid fynbos, ericaceous fynbos, restioid fynbos, asteraceous fynbos, and grassy fynbos.

Another important vegetation type of the Cape Region is renosterveld, a low shrubland occurring on richer soils originating from shale parent material. It is floristically differentiated from fynbos by the absence of restioids and the minor importance of proteoids. This community once covered more than a quarter of the Cape Region, but has now largely been cleared for agriculture and urban expansion.

Woodland and forest communities are surprisingly rare in the Cape Region. True forests occupy only about 3,850 square kilometers of moist sites (800–1,200 mm annual rainfall) along the southern coast that are relatively protected from fire. These forests are low in diversity and represent depauperate outliers of afro-montane forests of tropical East Africa.

The Cape Region contains arguably the most unique and diverse flora of any temperate area of the world. Its status as a distinct floral kingdom is reinforced by the presence of five endemic families—Geissolomataceae, Grubbiaceae, Penaeaceae, Roridulaceae, and Stilbaceae. Moreover, 193 endemic genera comprise 19.5 percent of the total.

Covering an area of only 78,500 square kilometers, the Cape Region contains about 9,000 species of vascular plants. The ten largest genera of the Cape Region account for over 20 percent of the flora, led by Erica (Ericaceae, 658 species) and Aspalathus (Fabaceae, 257 species). Other large genera are Phylica (Rhamnaceae), Agathosma (Rutaceae), Oxalis (Oxalidaceae), Pelargonium (Geraniaceae), Senecio (Asteraceae), Cliffortia (Rosaceae), Muraltia (Polygonaceae), and Ruschia (Aizoaceae-Mesembryanthema).

Levels of species endemism in the Cape floristic region are among the highest in the world. For the entire region, endemism at the species level is about 69 percent. The high levels of endemism present in the Cape Region are largely due to the presence of neoendemics rather than paleoendemic species. This dominance of neoendemics is indicated by the predominance of endemic diversity in large, species-rich genera, the widespread presence of sympatric congeners, and the edaphic specialization of many endemics on geologically young substrates. Rather than being a random ecological or phylogenetic assemblage of species, the great majority of endemics are low shrubs killed by fire and dependent on closely dispersed seeds for regeneration.

Four families are notably rich in endemics—the Proteaceae, Ericaceae, Rutaceae, and Polygalaceae. Species richness is greatest in the southwestern Cape Region centered around Cape Town. The Cape Peninsula, for example, supports 2,256 species (including 90 endemics) in an area of 471 square kilometers. Cape Hangklip on the eastern shore of False Bay near Cape Town has 1,383 species in 240 square kilometers.

Smaller regional centers of high endemism exist within the Cape Region. Dividing the Cape Region into five floristic zones on the basis of species distributions within seven large families, regional levels of endemism are highest in the southwestern and northwestern Cape (about 50 percent) and lowest in the eastern Cape and Inland Mountain regions with nonseasonal rainfall (18–28 percent). These patterns of regional endemism have been further demonstrated in studies of distribution of the Proteaceae in the Cape Region. For the entire Cape Region, 99.4 percent of the 330 species of Proteaceae are endemic. At a regional level, 63 percent of the Proteaceae in the southwestern region are endemic to that region, compared with only 19 percent for the Coastal Mountain and Southeastern Regions. Point endemism is also widespread involving species that are restricted to highly specific edaphic habitats.

Fynbos plant diversity is also extremely high at the alpha-diversity level of small stands. Typical fynbos communities support a mean of about 65 vascular plant species in 0.1 ha, with a range of 31–126 species reported. Renosterveld shrublands have even higher diversities with a mean of 84 species per 0.1 ha and a range of 28–143 species.

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 horstockii, which often lives in the flowers of the common arum lily (Zantedeschia aethiopica).

There are 34 native fish species in the Cape Region, 14 of which are endemic.

Human history in the Cape Region of South Africa dates back as much as 150,000 years, with evidence of active hunter-gatherer tribes in the region 21,000 years ago. Bushmen occupied the area until the seventeenth century, when European settlers arrived.

Although little or no agriculture was possible on the poor fynbos soils, the Dutch brought French Huguenot settlers in the late seventeenth century to produce wine grapes on the richer renosterveld soils. Many common garden bulbs, including gladiolus, watsonia, freesia, agapanthus, and calla lily, are native to this region.