Abstract This study aimed to quantify the morphological characters of Halophila ovalis and provide baseline information on the species' genetic characters (DNA chloroplast). The morphological data analyses employed the Excel 2016 Program combined with XL-STAT 2015 for the principal components analysis (PCA). The sequence data were analyzed using MEGA-X and version 6 DnaSP Program and compared with specimens of the Genbank. These were then used to construct the phylogenetic topology, nucleotide base composition, nucleotide base sequence, polymorphic sites, and haplotype. Seagrasses belonging to Halophila are typically small and narrow, less than 1 cm wide, and have a distinctive "straplike" shape with a pointed tip. The PCA identified four morphometric variables (leaf width, leaf length, petiole length, and rhizome diameter) related to PC1, which explains 51% of the observed variation. Species confirmation with the nBLAST technique found that the specimens were H. ovalis with the highest score and identity reaching 100%. The phylogenetic topology showed that H. ovalis from different coastal waters in Minahasa Peninsula occurred in a single clade with the GenBank metadata. Samples from various sites in Indonesia (including Bali) were identical to the recently studied H. ovalis reflecting low variability in nucleotide base sequences. Hence, H. ovalis specimens from the sites in this study showed high genetic connectivity. Key Words: DNA, genetics, morphology, phylogeny, seagrass.