Endemic mammals with continental relatives include the Zanzibar red colobus, one of Africa's rarest primates, the Zanzibar red colobus may number only about 1500. Isolated on this island for at least 1,000 years, the Zanzibar red colobus (Procolobus kirkii) is recognized as a distinct species, with different coat patterns, calls and food habits than related colobus species on the mainland.

Zanzibar red colobus live in a wide variety of drier areas of coastal thickets and coral rag scrub, as well as mangrove swamps and agricultural areas. About one third of the red colobus live in and around Jozani Forest- Ironically, the easiest monkeys to see are on farm land adjacent to the reserve. They are used to people and the low vegetation means they come close to the ground.

Rare native animals include the Zanzibar leopard, which is critically endangered and possibly extinct; and the recently described Zanzibar servaline genet. There are no large wild animals in Zanzibar, and forest areas such as Jozani are inhabited by monkeys, bush-pigs, small antelopes, civets, and, rumor has it, the elusive Zanzibar leopard. Various species of mongoose can also be found on the island. There is a wide variety of birdlife, and a large number of butterflies in rural areas. Pemba island is separated from Unguja island and the African continent by deep channels and has a correspondingly restricted fauna, reflecting its comparative isolation from the mainland. Its best-known endemic is the Pemba Flying Fox.