The free-living benthic copepods and nematodes in samples of decaying leaves and sediment, from a Rhizophora apiculata-dominated mangrove forest bordering the Sungai Merbok Estuary in north-western peninsular Malaysia, were identified to putative species. Analyses of community structure of these taxa revealed that both are concentrated within the surface layers of the sediment; communities associated with decomposing leaves are distinct from those associated with the sediment surface; and variation between physically similar sites within the forest is relatively small. It is suggested that the meiofaunal communities in tropical soft sediment mangrove estuaries respond primarily to salinity and exposure gradients as in temperate non-vegetated estuaries. Copepod communities of the Merbok mangrove system appear to be much more diverse than those in estuarine and saltmarsh habitats in other climatic regions, and detailed faunal analysis suggests that there is a high degree of species endemism, particularly in genera which are only found on decaying plant material.