This list of African species extinct in the Holocene covers extinctions from the Holocene epoch, a geologic epoch that began about 11,650 years before present (about 9700 BCE) and continues to the present. Africa is highly biodiverse; it is the continent with the largest number of megafauna species, as it was least affected by the extinction of the Pleistocene megafauna. However, a few species have disappeared from Africa as part of the ongoing Holocene extinction, driven by human activity. Madagascar and the Indian Ocean islands, Macaronesia, and Saint Helena, Ascension and Tristan da Cunha are biogeographically distinct from mainland Africa and have a much greater number of Holocene extinctions. Recently extinct species from these regions are listed in separate articles. Many extinction dates are unknown due to a lack of relevant information.

Mammals (class Mammalia)

Elephant-like mammals (order Proboscidea)

Elephants and mammoths (family Elephantidae)

Rodents (order Rodentia)

Old World rats and mice (family Muridae)

Possibly extinct

Primates (order Primates)

Lorises, pottos, and angwantibos (family Lorisidae)

Possibly extinct

True insectivores (order Eulipotyphla)

True shrews (family Soricidae)

Locally extinct

Carnivorans (order Carnivora)

Cats (family Felidae)

Locally extinct

Dogs (family Canidae)

Locally extinct

Bears (family Ursidae)

Locally extinct

Odd-toed ungulates (order Perissodactyla)

Horses and allies (family Equidae)

Possibly extinct

Rhinoceroses (family Rhinocerotidae)

Possibly extinct

Extinct in the wild

Even-toed ungulates (order Artiodactyla)

Pigs (family Suidae)

Right and bowhead whales (family Balaenidae)

Locally extinct

Gray whales (family Eschrichtiidae)

Locally extinct

True deer (family Cervidae)

Locally extinct

Cattle, goats, antelopes, and others (family Bovidae)

Extinct in the wild

Locally extinct

Birds (class Aves)

Landfowl (order Galliformes)

Guineafowl (family Numididae)

Possibly extinct

Bustards (order Otidiformes)

Bustards (family Otididae)

Possibly extinct

Shorebirds (order Charadriiformes)

Oystercatchers (family Haematopodidae)

Sandpipers (order Scolopacidae)

Auks (family Alcidae)

Hawks and relatives (order Accipitriformes)

Hawks, eagles, kites, harriers and Old World vultures (family Accipitridae)

Locally extinct

Passerines (order Passeriformes)

Cisticolas and allies (family Cisticolidae)

Reptiles (class Reptilia)

Squamates (order Squamata)

Plated lizards (family Gerrhosauridae)

Amphibians (class Amphibia)

Frogs (order Anura)

African torrent frogs (family Petropedetidae)

Possibly extinct

True toads (family Bufonidae)

Possibly extinct

Extinct in the wild

Ray-finned fish (class Actinopterygii)

Minnows and allies (order Cypriniformes)

Carps, minnows, and relatives (family Cyprinidae)

Salmon, trout and relatives (order Salmoniformes)

Salmon, trout and relatives (family Salmonidae)

Toothcarps (order Cyprinodontiformes)

Livebearers and relatives (family Poeciliidae)

Insects (class Insecta)

Butterflies and moths (order Lepidoptera)

Gossamer-winged butterflies (family Lycaenidae)

Bark lice, book lice, and parasitic lice (order Psocodea)

Family Linognathidae

Possibly extinct

Ostracods (class Ostracoda)

Order Podocopida

Family Candonidae