The Horn of Africa has been a renowned source of biological resources for thousands of years. The ancient Egyptians, Greeks and Romans sent expeditions and caravans to the region for frankincense, myrrh and other natural commodities to be taken back North along the incense route through the Arabian deserts.
Although research into the flora of the Horn of Africa is still ongoing, the best possible estimates are that there are about 5,000 species of vascular plants in the region, just over half of which—about 2,750 species —are endemic. There are strong concentrations of endemic species in northern Somalia and in the Socotra Archipelago.
For thousands of years, several native tree species have provided the raw materials for some of the Horn of Africa’s most important commodities, including frankincense (from Boswellia sacra in Somalia, Yemen and Oman, and B. frereana in Somalia), myrrh (from the widespread Commiphora myrrha and C. guidottii in Somalia and eastern Ethiopia) and dragon's blood tree or cinnabar (from the Vulnerable Dracaena cinnabari, found on Socotra). Dragon's blood tree is used as a medicine and dye. The production of frankincense and myrrh is still a major economic activity in Somalia and, to some extent, in Ethiopia and northern Kenya.
Hundreds of new species have been discovered in Somalia alone in the last 30 years, most notable among them the Somali cyclamen (Cyclamen somalense). Known only from a small area in northern Somalia, the plant was a surprising discovery in tropical Africa, as the genus Cyclamen is otherwise found only in the Mediterranean region.
Of the 697 bird species regularly recorded in the hotspot, 24 are endemic. Seven of these species are found only in Somalia.
One of the most notable endemic bird species in the hotspot is the Endangered Warsangli linnet (Linariajohannis), locally common in high, steep escarpments along the Gulf of Aden in northern Somalia. Another important flagship species is the Critically Endangered Djibouti francolin (Pternistis ochropectus), which is only found in two sites in Djibouti, Forêt de Day, which is thought to be the only viable site for this imperiled species, and the nearby Mabla Mountains.
Nearly 220 mammal species are found in the Horn of Africa, although only about 20 are endemic to the hotspot. The most notable endemics are several antelope species, including the beira (Dorcatragus megalotis), dibatag (Ammodorcas clarkei), Endangered Speke's gazelle (Gazella spekei) and silver dikdik (Madoqua piacentinii).
The hotspot is also home to the Critically Endangered Somali wild ass (Equus africanus somaliensis) and desert warthog (Phacochoerus aethiopicus).
The hamadryas baboon (Papio hamadryas), which was held sacred in ancient Egypt and often mummified, is today endemic to the hillsides and escarpments bordering the southern Red Sea and the Gulf of Aden.
The Horn of Africa's highest levels of endemism occur among reptiles, with more than 90 of around 285 species found nowhere else. The hotspot's six endemic reptile genera include Haackgreerius, a monotypic genus of skink found in Somalia, and Aeluroglena, which is represented by a single species of snake. Half of the endemic genera are restricted to Socotra, including the two Haemodracon gecko species and two snake genera, Ditypophis and Pachycalamus, represented by single endemic species.
Unlike the reptiles, amphibians are relatively poorly represented in the arid Horn of Africa, with nearly 30 species recorded, of which at least six are endemic. There is only a single endemic genus, Lanzarana, which is represented by one species, Lanza's frog (L. largeni) of Somalia. Despite suitable habitats, no amphibians are known to exist on Socotra.
There are an estimated 100 species of freshwater fish in the Horn of Africa, about 10 of which are endemic. These endemics include three cave-dwelling species found only in Somalia, two of which—the Somalian blind barb (Barbopsis devecchii) and Somalian cavefish (Phreatichthys andruzzii)—are blind.
No native freshwater fishes are known with certainty from Socotra, but populations of Arabian tooth carp Aphanius dispar have been introduced to some waters as part of an anti-malaria program.