By using a seine net, fish samples were taken from the nonestuarine Chwaka Bay (Zanzibar, Tanzania) from the mangroves, mud/sand flats and seagrass beds. Sampling was done twice per month between November 2001 and October 2002. In total, 150 fish species belonging to 55 families were identified. Diversity (H′) ranged from 1.9 in mud/sand flats to 3.4 within the Chwaka seagrass beds. Mean density of fishes was significantly higher in the mangrove creeks than in any other habitat (mean = 238.7 ind./1000 m2). Highest, but non-significantly different mean biomasses were recorded in the mangrove creeks (1.7 kg/1000 m2) and in the Marumbi seagrass beds (1.6 kg/1000 m2). The mangrove channel had the lowest biomass (0.6 kg/1000 m2). A high overlap in species composition (as high as 93.4% similarity) was found for adjoining habitats (i.e. mangrove creeks and mangrove channel), while habitats that were far apart showed low overlap (6.6% similarity for the Marumbi seagrass beds and mangrove creeks). On average, 58.4 and 63.2% in terms of abundance and biomass, respectively, of the fish assemblage of Chwaka Bay were of commercial fishery importance. Thus, Chwaka Bay appears to be an important juvenile habitat for various commercially important fish species.