The transboundary networks of Marine Protected Areas (MPAs) project, TRANSMAP, assessed local turnover and regional biodiversity across the East African Marine Ecoregion, where inter-governmental co-operation has been working to connect local MPAs. The benthic fauna in the three most dominant habitats on this coastlinebeaches, mangroves and seagrasses-were studied in two Regions (Northern Region, 10-13°S; Southern Region, 25-28°S). Meiofaunal taxa were used as the model faunal group owing to their diversity and abundance across habitat types and environmental conditions. Meiofaunal abundance averaged 2,500 individuals 10 cm -2 and was generally higher in mangrove and seagrass sediments than on the beaches, and was significantly different between habitats 9 Regions. In total, 18 taxa were recorded with highest diversity in the beach samples. Diversity indices and assemblage structure were significantly different between habitats, but also Regions.