Although the remaining forests scattered throughout the hotspot's 291,250 km² are typically tiny and fragmented, they contain remarkable levels of biodiversity. These forests also vary greatly in their species composition, particularly among less mobile species; for example, forests that are only 100 kilometers apart may differ in 80 percent of their plant species.
Within the hotspot, the region of highest endemism stretches from northern Kenya to southern Tanzania, possibly also including northernmost Mozambique. Two important subcenters of endemism are also recognized: the Kwale-Usambara subcenter of endemism on the Kenya-Tanzania border, and the Lindi subcenter of endemism in southern Tanzania.
There are about 4,050 vascular plant species in the Coastal Forests of Eastern Africa Hotspot and approximately 1,750 (43 percent) of the plant species are endemic. The hotspot holds at least 28 endemic plant genera, most of which are monotypic. About 70 percent of endemic species and 90 percent of endemic genera are found in forest habitats. Furthermore, about 40 percent of the endemic plant species are found in only a single forest; for example, the Rondo Forest in southern Tanzania has about 60 endemic species and two endemic genera.
Among the best-known plants in the hotspot are the species of African violets (Saintpaulia spp.). The 40,000 cultivated varieties of the African violet, which form the basis of a US$100 million/year house plant trade globally, are all derived from just three species found in coastal Tanzanian and Kenyan forests. The hotspot also contains 11 species of wild coffee, eight of which are endemic; none of these species has been exploited commercially.
More than 633 bird species occur in the hotspot; eleven of these are endemic. Pemba Island, which is one of BirdLife International's Endemic Bird Areas, has four endemic species: the Pemba white-eye (Zosterops vaughani), Pemba green-pigeon (Treron pembaensis), Pemba sunbird (Nectarinia pembae), and Pemba scops-owl (Otus pembaensis). The Tana River cisticola (Cisticola restrictus) is endemic to the Lower Tana River, and the Malindi pipit (Anthus melindae) is endemic to the coastal grasslands of Kenya. Most of the other endemics are found in the mainland coastal forest of Kenya and Tanzania, including the yellow flycatcher (Erythrocercus holochlorus), Sokoke pipit (Anthus sokokensis, EN), Clarke's weaver (Ploceus golandi, EN), and Mombasa woodpecker (Campethera mombassica).
Nearly 200 mammals are found in the Coastal Forests of Eastern Africa hotspot, and 11 of these are endemic, including the Ader's duiker (Cephalophus adersi, EN) from Zanzibar, Arabuko-Sokoke Forest and Boni-Dodori Forest, the Pemba flying fox (Pteropus voeltzkowi, VU) restricted to Pemba Island, the Kenyan wattled bat (Glauconycteris kenyacola), the Dar es Salaam pipistrelle (Pipistrellus permixtus), the golden-rumped elephant shrew (Rhynchocyon chrysopygus, EN), occurring in a narrow coastal strip in southeastern Kenya, and a recently described species of horseshoe bat (Rhinolophus maendeleo) in the Amboni Caves in Tanga District in Tanzania.
The primates are important flagship species for this hotspot. This relatively tiny hotspot boasts three endemic monkey species. Found only in small patches of gallery forest along the lower Tana River in Kenya, the Tana River red colobus (Procolobus rufomitratus, CR) is represented by only about 1,100-1,300 individuals, while the Tana River mangabey (Cercocebus galeritus, CR) has been reduced to only about 1,000-1,200 individuals. The Zanzibar red colobus (Procolobus kirkii, EN) has an estimated population of about 1,000-1,500 individuals, mainly in Zanzibar's Jozani Forest, but also in a number of village forests. The Zanzibar red colobus is a significant tourist attraction that, historically, was not hunted by the Muslim inhabitants of the Island; however, there have been recent reports that suggest it is being hunted by immigrants from the mainland. There are also two endemic species of galagos (out of a total of four occurring in the hotspot): the Rondo dwarf galago (Galagoides rondoensis) in the southern Tanzanian forests, the Kenya coast galago (G. cocos) from northern Tanzania and into Kenya.
The hotspot also still supports considerable populations of threatened large African herbivores, including black rhinoceros (Diceros bicornis, CR) and savannah elephants (Loxodonta africana, VU), especially in the larger protected areas and wilderness regions of southern Tanzania and northern Mozambique. There are also populations of African wild dog (Lycaon pictus, EN).
There are about 250 reptile species in the Coastal Forests of Eastern Africa Hotspot, and more than 50 of these are endemic. The hotspot has one endemic reptile genus, Scolecoseps, which is represented by three species.
The hotspot also has over 85 amphibian species, six of which are found nowhere else. These endemics include the Mafia Island toad (Stephopaedes howelli, EN), Shimba Hills banana frog (Afrixalus sylvaticus, EN), Shimba Hills reed frog (Hyperolius rubrovermiculatus, EN), and Phrynobatrachus pakenhami (EN), known only from northern Pemba, particularly Ngezi Forest Reserve. One species largely confined to the hotspot is Loveridge's snouted toad (Mertensophryne micranotis), the only member of its genus; this species is remarkable in that it is one of the few amphibians to breed by internal fertilization, although it still lays eggs, rather than giving birth to live young. In addition, a new genus of frog, similar to members of the genus Kassina, has recently been found in the Jozani Forest on Zanzibar and awaits description.
Nearly 220 fish species live in the fresh waterways of the Coastal Forests of Eastern Africa, and more than 30 of these are endemic. Of the 34 families represented in the hotspot, minnows (family Cyprinidae) are dominant, followed by killifishes (Nothobranchius spp.). Some species of fish have remarkable adaptations to survive in the hotspot's temporary coastal swamps and floodplains. For example, the air-breathing lungfishes Protopterus amphibious and P. annectens can survive in a dormant state for over a year in cocoons underneath dried mud.
Levels of endemism within some invertebrate groups are significantly higher than among vertebrates. About 80 percent of millipedes and 68 percent of mollusks are found nowhere else. The hotspot is also home to a Gondwana relict dragonfly species (Coryphagrion grandis) that has its nearest relatives in Central and Southern America.