The result showed that 12 out of 25 primers pairs produced clear polymorphic patterns and showed highly polymorphism due to locations and environment. According to the genetic relationship and cluster analysis, the phylogenetic tree was constructed and the similarity coefficient was 0.93. The phylogenetic tree was divided into 2 major groups (or 4 minor groups). The first major group, elliptic short leaf blade, was Halophila ovalis from Trad province. The second major group, having acuminate long leaf blade, included 5 species, namely Cymodocea serrulata, Halodule uninervis, H. pinifolia and Enhalus acoroides. Although the large variability of seagrasses within species and also between species was detected, the genetic diversity showed a correspondence with the morphological identification as well