There are two marine species in the genus Ozobranchus. Ozobranchus branchiatus mainly parasitizes green turtles and O. margoi parasitizes most turtle species. We used sequences for the mitochondrial cytochrome c oxidase subunit I gene (COI sequence analysis), along with morphological diagnosis, to compare the population genetic structures of O. branchiatus and O. margoi collected near Taiwan to those of their populations in the Atlantic. The results provide estimates of the genetic divergence between these leeches in the two regions. Ozobranchus branchiatus had a greater pairwise distance within Taiwan (0.0031–0.0141) than O. margoi (no differences). Phylogenetic tree analysis identified one O. branchiatus clade and one O. margoi clade in Taiwan. The better environmental adaptability and lower host specificity of O. margoi might result in lower genetic divergence among populations.