A survey was conducted to examine spatial variations in the population density of major meiofaunal taxa and the assemblage structure of free-living marine nematodes within 5 mangrove areas on the west and east coast of Zanzibar. Meiofauna densities in surface sediments (0–5 cm) ranged from 205 to 5263 ind. 10 cm2, being on average 1493 ind. 10 cm2. Of the 17 major taxa recorded, nematodes dominated (64–99%) in all samples while harpacticoid copepods were usually second most abundant. Within all areas the numbers of meiofauna were very variable and significant differences among areas were only detected for oligochaetes and turbellarians. Densities of nematodes, harpacticoids, polychaetes and turbellarians were, however, significantly (P<0.001) higher at low water stations compared with mid and high water stations. Harpacticoids were negatively correlated with the numbers of fiddler crab (Uca spp.) burrows. Other correlations between environmental factors (grain size, temperature, salinity, oxygen tension, prop root density, fiddler crab burrows) and major meiofaunal taxa were non-significant. A total of 94 nematode genera were recorded from four mangrove areas. The most abundant and frequent genera were Microlaimus and Spirinia, followed by Desmodora and Metachromadora. Representatives of the genera most common in current study are found all over the globe. There was a high variation in nematode assemblage structure within and between sampling areas indicating the absence of a well defined nematode assemblage confined to mangrove areas. In a hypersaline area diversity was much reduced and where salinity was over 100%. the fauna was restricted to 3 nematode genera, Microlaimus, Theristus and Bathylaimus. Multidimensional scaling ordination (MDS) of the nematode genera separated samples taken from low water stations from other stations, the assemblage structure being significantly different at the low water stations. Numbers of selective deposit feeders were negatively correlated with average grain size and positively correlated with silt content.