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Seagrasses are monocotyledons that grow in intertidal and subtidal zones. Seagrass beds are among ecosystems with the highest ecosystem service value. However, seagrass beds are rapidly decline due to anthropogenic disturbances and global climate change. Enhalus acoroides, a monoecious perennial species, is the largest seagrass in stature. It distributes in tropical regions, with Hainan Island as its northern limits. Clonal diversity and genetic structure of E. acoroides populations in Hainan Island were studied to facilitate its conservation and restoration. We used four polymorphic microsatellites to genotype samples collected from four extant populations. We found low clonal and genetic diversities within populations, consistent with the expectations of genetic structure in edge populations. A large range of genetic differentiation was found between these four populations, probably due to the large range of geographic distances between them and genetic drift by local extinction and recolonization. We found no sign of recent bottlenecks in all the populations, probably due to the within-population genetic diversity being too low to show obvious reduction even after bottlenecks. We proposed suggestions on population conservation for those with high priority. Given that seagrass bed had experienced rapid decline in recent years, strengthened conservation and ecological restoration are urgently needed.