Seagrasses, marine angiosperms, are widely distributed from subarctic to tropical coastlines of the world. Seagrasses provide several important ecological services in coastal ecosystems, including primary production, sediment stabilization and nutrient cycling. Recently, seagrass meadows have tended to decrease on a global scale due to human impacts and global environmental changes. Analyses that focus on the genetic features of seagrasses are imperative for establishment of effective conservation strategies of coastal ecosystems. In this study, we analyzed the genetic diversity and structure of sickle seagrass, Thalassia hemprichii in the Philippine Archipelago, where one of the most diverse bioregion in the world. A total of 1,339 T. hemprichii shoots that were collected from 33 meadows were genotyped using 9 polymorphic microsatellite markers, subsequently, 1,078 distinct multilocus genotypes were found. Clonal richness values varied widely among meadows. The results of STRUCTURE analysis showed that the meadows among the Archipelago were generally divided into two groups, Northwestern and Southeastern. This result indicated that the genetic structure among the Archipelago may infer the patterns of sea currents surrounding this area.