This study deals with the relation between tropical meiofauna and environmental variables by comparing the 'benthic' (i.e. in the bare sediment adjacent to seagrass plants) and the 'epiphytic' (i.e. in samples including seagrass plants) meiofauna associated with five seagrass species from the high intertidal to the high subtidal zone in Gazi Bay (Kenya), Ordination and variance analysis revealed three distinct 'benthic' and two 'epiphytic' meiofauna assemblages. These assemblages corresponded entirely with those identified for the seagrass species: a high intertidal pioneer association (Halophila ovalis/Halodule wrightii), an intertidal climax assemblage (Thalassia hemprichii) and a high subtidal pioneer association (Halophila stipulacea/ Syringodium isoetifolium). These data support the hypothesis that meiofaunal communities correspond to the characteristic zonation of the seagrass vegetation in Gazi Bay. In beds of the pioneer seagrass species, the close relationship between sediment characteristics and both 'benthic' and 'epiphytic' meiofauna communities suggests that these pioneer communities were mainly driven by physical factors. The 'benthic' communities adjacent to the climax seagrass species T. hemprichii were more structured by biogenic factors, e.g. \% TOM, chlorophyll a and c, fucoxanthin, habitat complexity and growth form of the seagrass species. For its associated 'epiphytic' meiofauna the latter conclusion was even more striking. These data corroborate the importance of physical factors in disturbed environments (intertidal zone, near pioneer seagrasses) and of biotic factors in more stable conditions (subtidal zone, near climax seagrasses). © 2001 Elsevier Science B.V.