Abstract: Seagrasses are angiosperms that are thought to have become adaptive to aquatic environment independently. The marine, monocotyledonous Zostera marina is a species of Zosteraceae using traditional classifications, which widely distributes from subtropical to subfrigid coastal oceans. seven natural populations of Z. marina (Lidao, Tian'ehu, Qingdao Bay, Dalian, Naepo, Tokyo Bay and Finavarra) were used in this study. To study the mechanism of the genetic diversity and population structure of the seven populations, microsatellite marker (SSR) analysis was done. A total of 57 alleles were identified in 148 individuals across the four microsatellite primers analyzed, with a mean value of 6 alleles per locus. The mean expected heterozygosity (He) and observed heterozygosity (Ho) across all populations were 0.687 and 0.417, respectively, and a higher level of diversity was found in the population from the Qingdao Bay (A=7.750, AR=7.043) than other populations. The minimum Fst value was 0.051 between the populations from the Qingdao Bay and Dalian. The maximum Fst value was 0.261 between the populations from Tian'ehu and Finavarra. The Fst values suggested moderate genetic differentiation within most of the Z. marina populations. From the UPGMA tree, four populations in China (Lidao, Tian'ehu, Qingdao Bay and Dalian) clustered together, and the genetic relationships may be attributed to eelgrass meadow fragmentation. The geographic distance was responsible for the genetic differentiation from large-scale among populations in China (Lidao, Tian'ehu, Qingdao Bay and Dalian), Korea (Naepo), Japan (Tokyo Bay) and Ireland (Finavarra). Results of possible number of clusters supported that this seagrass species originated from East Asia. The population from the Qingdao Bay has higher genetic diversity, suggesting that populations in this region demand prioritized conservation and utilization for breeding programs.