The present study was undertaken with the objective to investigate the intraspecific variation of Channa punctatus on the basis of morphometric characters using the truss network system that was constructed from the fish body. Fish samples were collected from the Narora (n = 62) and Kanpur sites (n = 46) of the Ganga River, the Firozabad site in the Yamuna River (n = 66) and at the Lucknow site of the Gomti River (n = 60). Data were subjected to principal component analysis, discriminant function analysis and univariate analysis of variance. The first principal component (PC I) analysis explained 47.75% of total variation while PC II and PC III explained 8.18 and 7.48%, respectively. The step-wise discriminant function analysis retained seven variables that significantly discriminated the populations. Using these variables 81.85% of the original groups were classified into their correct samples. Misclassification was higher for the samples from Ganga River (19.6% at the Kanpur site and 19.4% for the Narora site). Of the total 27 transformed morphometric measurements, 23 exhibited significant differences among the populations. These findings indicate the presence of different stocks of fish from the three rivers.