1. Genetic identity values among 6 populations ranging from 0.66-0.92.
2. The genetic diversity of Z. marina L. showed 83.29% among populations and 16.71% within populations.
3. The migration pattern with gene flow showed less differentiation between Tian’ehu and Lidao.
4. According to this research, AFLP marker is suitable for genetic diversity and conservation in seagrass species.