Puntius sensu lato has many species but is seen as an artificial grouping for unrelated cyprinids. The correct taxonomic identification and taxonomic status of the Puntius complex have been challenged due to their minor morphological differences. This study investigates the morphological variation and taxonomic validity of 10 species within the Malay Puntius complex using an integrative approach. In the traditional analysis, a one-way analysis of variance (ANOVA) revealed that 28 out of 30 traits (20 morphometric and 10 meristic characters) were significant. Discriminant function analysis (DFA) indicated significant morphological variation among morphotypes, particularly in meristic traits. This analysis correctly classified 82.8% of the originally grouped and 74.5% of the cross-validated groups based on meristic characters. Truss analysis indicated that 14 out of 22 characters were significant (p < 0.05). The geometric morphometric analysis was largely consistent with the morphometric and truss analyses, confirming the validity of the distinct species. Molecular phylogenetic analyses of mitochondrial COI gene sequences confirmed the validity of all species. However, consistent with morphological data, they also supported the non-monophyly of the genus Barbonymus.

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