Twenty stations were sampled in a reef-protected lagoon on the east coast of Zanzibar from a variety of habitats: seagrass beds, fine sand, bare medium sand and coarse sand. Total meiofauna densities ranged from 219 to 3422 ind./10 cm2. Stations in the upper lagoon (< 400 m from shore) had relatively higher densities of meiofauna than those of other habitats, apart from seagrass beds. Of the 12 major taxa recorded, Nematoda normally was the most abundant taxon, contributing between 13% and 97% of total fauna, followed by Harpacticoida, Polychaeta and Turbellaria. Nematodes were dominated by epistrate feeders in all habitat-types and altogether 100 nematode genera were found within the lagoon. Clear nematode assemblage structures were depicted by non-metric multidimensional scaling ordination in seagrass bed, fine sand and coarse sand habitats. On a larger scale, sediment characteristics seem to determine the gross assemblage structure. Samples from the same station were more similar in terms of generic occurrence and population structure than samples from different stations in similar habitats. This indicates that there are localised factors influencing the nematode populations on a small scale in each habitat-type.