The relative importance of bay habitats, consisting of mangrove creeks and channel, seagrass beds, and mud and sand flats, as feeding grounds for a number of fish species was studied in Chwaka Bay, Zanzibar, Tanzania, using gut content analysis and stable isotope analysis of carbon and nitrogen. Gut content analysis revealed that within fish species almost the same food items were consumed regardless of the different habitats in which they were caught. Crustaceans (mainly copepods, crabs and shrimps) were the preferred food for most zoobenthivores and omnivores, while fishes and algae were the preferred food for piscivores and herbivores, respectively. The mean d13C values of fishes and food items from the mangrove habitats were significantly depleted to those from the seagrass habitats by 6 9 and 9 7% for fishes and food items, respectively, and to those from the mud and sand flats by 3 5 and 5 8%, respectively. Fishes and food items from the mud and sand flats were significantly depleted as compared to those of the seagrass habitats by 3 4 and 3 9%, for fishes and food, respectively. Similar to other studies done in different geographical locations, the importance of mangrove and seagrass themselves as a primary source of carbon to higher trophic levels is limited. The different bay habitats were all used as feeding grounds by different fish species. Individuals of the species Gerres filamentosus, Gerres oyena, Lethrinus lentjan, Lutjanus fulviflamma, Pelates quadrilineatus and Siganus sutor appeared to show a connectivity with respect to feeding between different habitats by having d13C values which were in-between those of food items from two neighbouring habitats. This connectivity could be a result of either daily tidal migrations or recent ontogenetic migration. # 2006 The Authors Journal compilation # 2006 The Fisheries Society of the British Isles