The common seagrass, Halophila ovalis (R. Brown) J.D. Hooker, is highly variable morphologically. It adapts well to various environmental conditions rendering the various forms unclear taxonomically. Halophila species were collected along the coast of southern Thailand. The morphology was quantified according to different parts of the leaf and the ages of leaves. Some samples had significantly different characters from H. ovalis: the lengths of their leaves ranged from 11.7-29.4 mm, and the widths from 5.6-14.8 mm; there were 9-18 cross veins. Phylogenetic analyses based on ribosomal internal transcribed spacer sequences divided them into two groups: one agrees with H. ovalis and the other with H. major. We suggest that leaf size at maturity (age iii-iv) and the ½ ratio between the leaf width and the space between the intra-marginal vein and lamina margin are important characters that distinguish Halophila species.