Coral reefs are well developed in many places. Close to the mainland there are fringing and patch reefs along much of the coast to the north of the Pangani River, with a wide lagoon with only occasional patch reefs further south around Dar es Salaam. Coral cover is highly varied, with estimates on different patch reefs varying between 1 and 80 percent. Clearly in some areas reefs are not actively developing, and represent little more than occasional coral growth on Pleistocene reef deposits. Coral diversity increases with distance from the coast, and up to 39 genera of coral have been reported from individual patch reefs off the Tanga coast. Fringing reefs begin again off the mainland coast south of the Rufiji Delta and are very well developed, with deep spur and groove formations on outer slopes. These are particularly well represented in the areas around and to the south of Mtwara where undamaged reefs, especially those further offshore, often show over 50 percent live coral cover.

Offshore reefs are highly developed around the main three islands, their associated islets, and the Songo Songo Archipelago in the south. Reefs around parts of Pemba are prolific, with corals recorded to 64 meters, and cover on western reef slopes at 21-60 percent. Cover tends to be low (rarely above 15 percent) on eastern shores of all the larger islands, probably due to the very high wave energies which impact these coasts. Misali Island, just west of Pemba, has been singled out for having some of the highest recorded coral cover, and high species diversity with 40 genera of coral and 350 fish species. Chumbe and Mnemba islands off Zanzibar have been similarly singled out as offshore islands with diverse and well protected reefs. It is possible that similar diversity may be recorded from other reefs, many of which have yet to receive detailed scientific attention. Mafia Island has extensive reefs, particularly in the south, many of which remain in good condition. Some 380 fish species and 45 coral genera have been recorded from this area. Likewise there are many important reefs around the Songo Songo Archipelago, with the slightly deeper reefs, and those furthest from the mainland, remaining in good condition. Finally, Latham Island (Fungu Kisimkasi) is a tiny island with an associated fringing reef system lying off the continental shelf some 80-100 kilometers east of the mainland south of Dar es Salaam. There are no detailed descriptions of the reefs but the island has some very important bird colonies.

Tanzanian coast with fringing and patch reefs on a narrow continental shelf. The main reefs occur around Unguja (Zanzibar), Pemba and Mafia islands, and along the mainland at Tanga, Pangani, Dar-es-Salaam, Mkuranga, Kilwa (including the extensive Songo Songo Archipelago), Lindi and Mtwara.