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All five islands of the archipelago – Mafia, Jibondo, Juani, Chole and Bwejuu – have lush vegetation and wildlife, with coconut palms, baobabs, cashew, mango and papaya trees in the interior. These are home to bush babies, wild pigs, blue duikers, genets, vervet monkeys and Pteropus fruit bats (flying foxes). On the coast, mangrove forests and tidal flats attract endless sea birds.

In 1995 Mafia Island had financial help from the WWF to make a natural marine wildlife centre which led to establishment of the first Marine Park in Tanzania. Today there are more than 50 species of coral, including giant table corals, huge stands of blue-tipped staghorn corals, and over 400 species of fish.

Birdlife on Mafia Island is also distinctly different that mainland with a range of sea birds and forest birds. Of special interest are the coastal birds, with many different waders, as well as fish eagles, palm nut eagles and open-billed storks. There are also at least five different varieties of sunbird.

Interestingly, the popular rumours of a pygmy hippo on the island were confirmed by the Tanzania Tourist Board in 2013 after being spotted by two tourists.