Correct assessment of freshwater fishes depends on the most recent taxonomic nomenclature and accurate identification. The existing of the complex between closely related species is one of the prominent issues that sometimes poorly addressed that leads to misidentification of the species and inaccurate diversity measurement. This study addressed the issue through morphometrics methods, to correctly evaluate the diversity of freshwater fish within species group of genus Barbodes , i.e., B. binotatus and B. banksi . In examining species complex of B. binotatus and B. banksi , traditional and landmark-based geometric morphometrics methods were applied. Traditional morphometric displayed characters that distinguished both species were generally located at the anterior part of the body, and specifically in the cephalic area of the fish. Landmark-based geometric morphometric revealed a highly similar body shape on both species. Variations within both species were subtle and could not be significantly distinguished by both methods. The overall outcomes of this study suggest that in order to achieve a proper assessment to freshwater fishes, one need to solve the identification problems in species complex. This effort could consequently lead to a better understanding of freshwater fish status, for a better conservation plan and management.