Fringing mangrove forests are common in coastal areas on island systems. They are discretely distributed, limited in population size, and directly impacted by tides and waves. Thus, they are considered vulnerable to stress caused by sea-level rise and coastal development. Despite the high ecological and socioeconomical importance of mangrove ecosystem, the rate of habitat loss has been significant especially in island systems. Though understanding the local connectivity and nearshore hydrodynamics is important for management and conservation, they are understudied for mangrove ecology. Our study will discuss how seascapes in Okinawa island systems affect the dispersal patterns of Rhizophora stylosa. R. stylosa, a representative species of the family Rhizophoracea, is a mangrove species common throughout the Okinawa islands and abundant throughout the Indo-West Pacific. Using 12 microsatellite markers, the landscape genetics showed clear clustering and migration patterns both within and amongst islands. The genetic results were compared with physical oceanographic data collected from in-situ Lagrangian experiments. Our genetic results suggest that R. stylosa dispersal is primarily limited within local region, and our oceanographic data agreed. Additionally, both genetic and oceanographic data suggest consistent but rare dispersal patterns. As a conclusion, habitat recovery may be difficult in island systems.