Genetic diversity and population genetic structure of Excoecaria agallocha, a typical mangrove associate species,were surveyed at divergent habitats (intertidal and inland). In general, intertidal populations had higher genetic diversity than inland populations. Genetic differentiation among intertidal populations (G(ST) = 0.191) were smaller than that among inland populations (G(ST) = 0.218), suggesting that gene flow via seed among intertidal populations were stronger. In an analysis of molecular variance (AMOVA), we found that 15.13% of the genetic variance could be explained by the differentiation between habitats, as compared to only 11.63% to geographical effects among five sits 181 -759 km distant from each other. This implies that markedly selection regimes result in habitat adaptation. Isolation-by-distance, Southwest Monsoon Current,China Coastal Current and genetic drift played important role in genetic differentiation of China population of Excoecaria agalocha.