Most species identification inTrichopodus trichopterusis primarily based on phenotypic variation of the body, including color polymorphisms, specific markers, and size differences. These key attributes can sometimes be difficult to apply due to ontogeny development, environment interaction, and specimen quality. Therefore, this study aimed to determine intraspecific variation ofT. trichopterusbody conformation using truss morphometric analysis. The fish specimens used were collected from the museum in Sumatra (n = 31), Java (n = 30), Kalimantan (n = 30), and Sulawesi (n = 35). Truss measurement data were subjected to univariate and discriminant function analysis (DFA). The results showed that 5 measured characters were significant discriminators among the observed populations (P < 0.05). The initial classification accuracy was 54.2%, marginally decreasing to 46.6% after cross-validation. Based on geographic distributions, Kalimantan specimens had the highest classification at 96.7%, followed by Sulawesi, Java, and Sumatra at 94.3%, 94.1%, and 91.2%, respectively. Further investigation revealed that habitat differences had a significant impact on morphometric characteristics. In conclusion, differences were observed in the morphological characters of the T. trichopterus populations in Indonesian water.