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Previous examination of the mitochondrial <i>NADH2</i> gene and morphological characteristics led to the resurrection of <i>Scoliodon macrorhynchos</i> as a second valid species in the genus, in addition to <i>S. laticaudus</i>. This study applied an integrated taxonomic approach to revisit the classification of the genus <i>Scoliodon</i> based on new materials from the Malaysian Peninsula, Malaysian Borneo and Eastern Bay of Bengal. Mitochondrial DNA data suggested the possibility of three species of <i>Scoliodon</i> in the Indo-West Pacific, while the nuclear DNA data showed partially concordant results with a monophyletic clade of <i>S. macrorhynchos</i> and paraphyletic clades of <i>S. laticaudus</i> and <i>S.</i> cf. <i>laticaudus</i> from the Malacca Strait. Morphological, meristic and dental characteristics overlapped between the three putative species. Collective molecular and morphological evidence suggested that the differences that exist among the non-sympatric species of <i>Scoliodon</i> are consistent with isolation by distance, and <i>Scoliodon macrorhynchos</i> remains as a valid species, while <i>S.</i> cf. <i>laticaudus</i> is assigned as <i>S. laticaudus</i>. The Malacca Strait acts as a spatial delineator in separating the Pacific <i>S. macrorhynchos</i> (including South China Sea) from the Northern Indian Ocean <i>S. laticaudus</i>. Future taxonomic work should focus on clarifying the taxonomic status of <i>Scoliodon</i> from the Indonesian waters.