A population of about 25,000 large animals, largely ungulates along with the highest density of mammalian predators in Africa, lives in the crater. These include black rhinoceros Diceros bicornis (CR), which have declined from about 108 in 1964-66 to between 11-14 in 1995, and hippopotamus Hippopotamus amphibius which are very uncommon in the area. There are also many other ungulates: wildebeest Connochaetes taurinus (7,000 estimated in 1994), zebra Equus burchelli (4,000), eland Taurotragus oryx, Grant’s and Thomson’s gazelles Gazella granti and G. thomsoni (3,000). The crater has the densest known population of lion Panthera leo (VU) numbering 62 in 2001. On the crater rim are leopard Panthera pardus, elephant Loxodonta africana (EN) numbering 42 in 1987 but only 29 in 1992, mountain reedbuck Redunca fulvorufula and buffalo Syncerus caffer (4,000 in 1994). However, since the 1980s the crater’s wildebeest population has fallen by a quarter to about 19,000 and the numbers of eland and Thomson’s gazelle have also declined while buffaloes increased greatly, probably due to the long prevention of fire which favors high fibrous grasses over shorter less fibrous types.
In summer enormous numbers of Serengeti migrants pass through the plains of the reserve, including 1.7 million wildebeest, 260,00 zebra and 470,000 gazelles. Waterbuck Kobus ellipsiprymnus mainly occur mainly near Lerai Forest; serval Felis serval occur widely in the crater and on the plains to the west. Common in the reserve are lion, hartebeest Alcelaphus buselaphus, spotted hyena Crocuta crocuta and jackal Canis aureus. Cheetah Acinonyx jubatus (VU), though common in the reserve, are scarce in the crater itself. Wild dog Lycaon pictus (EN) has recently disappeared from the crater and may have declined elsewhere in the Conservation Area as well. Golden cat Felis aurata has recently been seen in the Ngorongoro forest.
Over 500 species of bird have been recorded within the NCA. These include ostrich Struthio camelus, with white pelican Pelicanus onocrotalus, and greater and lesser flamingo Phoenicopterus ruber and P.minor on Lake Makat in Ngorongoro crater safari, Lake Ndutu and the Empakaai crater lake where over a million birds forgather. There are also lammergeier Gypaetus barbatus, Ruepell’s griffon, Gyps ruepelli (110) Verreaux’s eagle Aquila verreauxii, Egyptian vulture Neophron percnopterus, pallid harrier Circus macrourus, lesser falcon Falco naumanni (VU), Taita falcon F. fasciinucha, kori bustard Choriotis kori, Fischer’s lovebird Agapornis fischeri, rosy-breasted longclaw Macronyx ameliae, Karamoja apalis Apalis karamojae (VU), redthroated tit Parus fringillinus and Jackson’s whydah Euplectes jacksoni. Sunbirds in the highland forest include the golden winged sunbird Nectarinia reichenowi and eastern double collared sunbird N. mediocris. Other waterbirds found on Lake Eyasi include yellowbilled stork Mycteria ibis, African spoonbillPlatalea alba, avocet Recurvirostra avosetta and greyheaded gull Larus cirrocephalus. The butterfly Papilio sjoestedti, sometimes known as the Kilimanjaro swallowtail, flies in the montane forests. It has a very restricted range but is well protected in national parks.