Abstract: Biodiversity differentials between macrobenthic assemblages associated with adjacent intertidal and subtidal areas of a single seagrass system were investigated for the first time. Assemblage metrics of conservation relevance—faunal abundance and its patchiness, faunal richness, and beta diversity—were examined at four contrasting dwarf-eelgrass localities in the Knysna estuarine bay, part of South Africa's Garden Route National Park but a system whose intertidal areas are heavily impacted anthropogenically. Faunal assemblages were significantly different across all localities and between subtidal and intertidal levels at each locality although their taxonomic distinctness was effectively constant. Although, as would be expected, there were clear trends for increases in overall numbers of species towards the mouth at all levels, few generalities relating to the relative importance of the subtidal seagrass habitat were evident across the whole system—magnitude and direction of differentials were contingent on locality. Shore-height related differences in assemblage metrics were minor in the estuarine and lagoonal zones but major in the marine compartment, although the much greater subtidal faunal abundance there was largely consequent on the superabundance of a single species (the microgastropod Alaba pinnae), intertidal zones then displaying the greater species diversity due to greater equitability of species densities. Along its axial channel, the Knysna subtidal seagrass does not support richer versions of the intertidal polychaete-dominated assemblages fringing it; instead, it supports different and more patchily dispersed gastropod-dominated ones. At Knysna at least, the subtidal hardly constitutes a reservoir of the seagrass biodiversity present intertidally.