Habitat utilisation by juveniles of 13 commercially important fish species was studied in five habitats located in Chwaka Bay, Zanzibar: mangrove creeks, mangrove channel, sand/mud flats, a seagrass area close to mangroves, and a seagrass area far from mangroves. Fish samples were collected from each habitat using a seine net, and fish abundance and size were measured to determine habitat utilisation. The seagrass beds near to mangroves showed the most diverse fish assemblage of all habitats, possibly because it functions as a corridor between the mangroves and deeper parts of the embayment. Juveniles of Cheilio inermis, Hipposcarus harid, Leptoscarus vaigiensis, and Scolopsis ghanam inhabited seagrass beds only. Juveniles of Gerres filamentosus and Monodactylus argenteus were mainly found in the mangrove habitats. Lethrinus variegatus, Pelates quadrilineatus and Siganus sutor were found in more than two habitats, with highest abundances in seagrass beds. Juveniles of Gerres oyena, Lethrinus lentjan, Lutjanus fulviflamma and Sphyraena barracuda were the most generalist species and were found in all studied embayment habitats. Visual census surveys supported the seine net data showing that most fishes in the embayment habitats were juveniles or sub-adults. In terms of habitat utilisation by different size classes, five of the 13 species (Lethrinus lentjan, L. variegatus, P. quadrilineatus, Siganus sutor and Sphyraena barracuda) were found as small-sized individuals in shallow and turbid mangrove areas, whereas large-sized individuals were observed in deeper and less turbid seagrass beds. A possible explanation for this pattern could be an ontogenetic shift in habitat utilisation, although this could not be proven. The patterns observed in the present study show a high similarity to those observed in marine embayments in the Caribbean, indicating that similar mechanisms are at work which make these systems attractive juvenile habitats.