Abstract The genetic relationship of Zostera marina was analyzed by AFLP marker. A total of 235 bands were detected from 63 individuals by 6 primer combinations, of which, 160 (68.09%) loci were polymorphic. The highest Nei's gene diversity value (H) and Shannon's information index value (I) were detected in population Clare (H = 0.072, I = 0.115), while the lowest were observed in population Jiaonan (H = 0.007, I = 0.011). Genetic identify values among 6 populations ranging from 0.66 to 0.92 were observed with the corresponding distance values ranging from 0.076 to 0.340. The results of AMOVA showed 83.29% genetic variation was found among populations and 16.71% within populations. According to UPGMA tree, population Tian'ehu was genetically closer to population Jiaonan than population Lidao, which might be attributable to eelgrass meadow fragments and some marine gyres/currents. The geographic distances were responsible for the genetic differentiation among populations from China, Japan, Korea and Ireland. The results of the present study emphasized the utility of DNA-based markers for conservation in genetically depauperate species, any future restoration and conservation projects locally used eco-sourced materials for population augmentations.