The primary threat to the biodiversity of the Eastern Afromontane Hotspot is habitat loss, due to conversion of land for agriculture, plantations and commercial estates, as well as logging. Other threats include fires, mining, infrastructure development gathering of firewood, and collection of plants for medicinal use, while hunting and disease have led to major declines in the populations of many species. It is estimated that only about 10 percent of the hotspot's original vegetation remains in pristine condition.
In the Eastern Arc Mountains and Southern Rift, large areas of mountain forest and grassland were cleared during colonial times for commercial estates growing tea, coffee, and pine trees, or for cattle ranches. More recently, forests have been cleared for banana, bean, and tree tomato farms, while grasslands are converted to cropland for beans, potatoes, and pyrethrum. Former grasslands have also been used for softwood plantations, growing exotic species such as pines. In Tanzania and Malawi, high human populations densities and rapidly increasing populations have exacerbated the pressure for subsistence agricultural land.
The Eastern Arc Mountains also contain a number of valuable timber species, which have been logged on these mountains for more than a century. While almost all of this logging is illegal, it has proved difficult to eliminate. Other threats to these forests include the collection of firewood, charcoal production, hunting, and gathering plants for medicine. Intentional burning has been responsible for converting much of the Afromontane forests in the region to grassland and scrub-grassland. In addition, artisanal mining for gold, rubies and garnets poses a threat to some areas.
The Albertine Rift has some of the highest human population densities on the African Continent, with up to 750 people per square kilometer in parts of Rwanda and Uganda. Consequently, much of the land was long ago converted to agriculture and pressures on the remaining lands are enormous. People use forest products for many necessary materials, including rope, bean stakes, firewood, timber, medicines, fruit, bushmeat, and honey. Fires also pose a threat to remaining forest areas.
Bushmeat consumption is also on the rise in the Albertine Rift, as soldiers return from the Congo to Rwanda and Uganda who have developed a taste for bushmeat in the absence of any alternative sources of protein. Poaching poses a threat to elephants, hippos, buffalos and larger antelope species in the savanna parks in Uganda and the DRC, while snares set by hunters have resulted in a quarter of the chimpanzees in Uganda having maimed limbs, including missing hands and feet. Insecurity and civil strife in the Great Lakes region has also led to the degradation and loss of protected areas, as militia groups have used them to hide in and launch attacks on nearby inhabitants. There has been a significant loss of trained protected-area staff; more than 100 staff were killed in protected areas in eastern DRC in the last six years, and a third of the staff working with gorillas in Rwanda were killed between 1990 and 1999.
Population pressure is also a problem in the Ethiopian Highlands; the population of Ethiopia has increased tenfold in the last 60 years. Eighty percent of the countrys 70 million people live in the highlands, putting significant pressure on the land for agricultural development. Ethiopia also has the largest national herd of domestic livestock, and cattle in particular, in Africa. This livestock is increasingly using the most extreme areas to graze, and overgrazing has led to erosion, an increasing abundance of unpalatable or poisonous species, and heightened competition between livestock and wildlife. Hunting is also a significant problem in the Ethiopian Highlands.