Indonesia, home to a significant portion of the world’s fish biodiversity, faces challenges in accurately identifying and conserving its freshwater fish species, including Ompok hypophthalmus. This study examines the morphological and molecular identification status of O. hypophthalmus, highlighting inconsistencies in taxonomic practices and the need for integrative approaches. Morphological studies, such as those by Ng (2003), identified three distinct species within the O. hypophthalmus group, yet subsequent research often misclassified O. rhadinurus and O. urbaini as O. hypophthalmus. Molecular analyses, including DNA barcoding of cytochrome oxidase I (COI) and cytochrome b (Cyt b) genes, revealed significant genetic divergence among populations from different Indonesian rivers, suggesting speciation or misidentification in prior studies. Phylogenetic and genetic analyses confirmed the presence of O. hypophthalmus in Arut River, while Indragiri and Tapung Rivers were dominated by O. rhadinurus. These findings emphasize the importance of integrating morphological and genetic tools to resolve taxonomic ambiguities and support effective fish management and conservation strategies. This study provides critical genetic data, advocates for molecular methods in biodiversity assessments, and underscores the ecological significance of accurately identifying native and invasive fish species in Indonesia and World.