Given that the biodiversity of Southern Africa is remarkably intact, the most immediate challenge is to avoid degradation of habitat in the extensive areas that are used for activities such as livestock ranching, while simultaneously maintaining viable livelihoods for the people who live in these areas.
The invasion of ecosystems by alien species has caused significant economic losses. Such species have been deliberately or accidentally introduced by humans. Only a fraction of such introductions become problem species, but when they do the consequences can be severe for local biodiversity, ecosystem services and human well-being. For instance, it has been calculated that the additional water use by alien trees in South Africa (excluding those in plantations and orchards) is between 1,400 and 3,300 million m3/year. The article Invasive alien species in Africa looks at these issues more closely.
Climate change is also emerging as a major threat to biodiversity in Southern Africa, with some symptoms already manifest. While extreme climate variation is not new, the magnitude and rapidity of climate change likely to occur in the 21st century is greater than the capacity of many organisms to respond by adaptation or migration. Migration to areas with a suitable climate is severely hampered by barriers such as roads, fences, urban areas and cultivated fields. The highly diverse and unique succulent flora of the winter-rainfall regions in the southwest of Africa is projected to be particularly threatened, and emerging evidence suggests the effects of climate change are already apparent.