Areas with the highest number of species are dispersed throughout the country, often in localised areas where several different habitats are found close together, or in areas of transition between major habitats or climates. Many of these areas are associated with highlands or isolated hills because of their varied microhabitats (relief, slopes, soils and rocks). The Namusberge north of the Orange River between Oranjemund and Noordoewer provide a good example of this where the plains lead into mountains, fog penetrates up into the valleys and rain may fall in any month.

As is the case elsewhere in the world, Namibia's endemics are most abundant in areas associated with variations in altitude, substrate or topography, which provide numerous microclimates. Highlands of importance for endemic plants include the Brandberg, Khomas Hochland, Karas Mountains, western escarpment, and the numerous inselbergs in the southwest. Many endemic plants are also associated with a specific or isolated substrate, such as the limestones of the Otavi–Grootfontein–Tsumeb hills or the granites of the Brandberg.

Some endemic species are widespread, but others occur in very limited areas (figure 6.07). Certain life forms of endemics may be concentrated in particular areas too. For example, the endemics of the southwestern parts of Namibia are mainly succulents while further inland, east of the Huns Mountains, endemic dwarf shrubs are more common. The Kaokoveld is the only area in Namibia with a few endemic trees.

This map shows the number of endemic species that occur in no more than two adjacent quarter-degree squares. These endemic species have extremely localised distributions, usually occur in small numbers and are adapted to the specific environmental conditions in these areas. They therefore have particular conservation value. The majority are found in western Namibia, but also in the central regions associated with high elevations.

The geographic distributions of many unrelated plant species overlap in ways that suggest that they share similar origins, for example having evolved at similar times or in similar areas and/or environmental conditions. Most of Namibia's 4,000 plant species can be classed into nine floristic groups, each with a similar evolutionary history. These floristic groups differ from those of vegetation types (figure 6.02) in which plants share ecological requirements and growth forms. Each floristic group has plants endemic to it, as well as species that occur only here and then outside Namibia. The grouping of plants in the cream-coloured area of the map has yet to be understood.

Up to 200 species co-occur in the Welwitschia Desert group, over 150 in the Southern Succulent Desert group and at least 100 species are confined to the Huns–Orange group. Evidence suggests that the Huns–Orange group contains the oldest flora of Namibia (from more than 20 million years ago) followed by the Welwitschia Desert (17 million years ago).

Certain plants in Namibia also occur, or have close relatives, in separate populations in eastern southern Africa and northeast Africa. The same is true for many animals, such as oryx and ostriches. All these organisms were probably once continuously distributed between these areas.