Morphological variations of the Asian sheat catfish, Wallago attu (Bloch and Schneider, 1801) sampled from the rivers Gomti, Ganga, Yamuna at Lucknow, Kanpur and Agra districts in Northern India, river Hooghly at Kolkata in Eastern India and river Pampa at Kerala in Southern India were analyzed in the present study. Images of 261 specimens of W. attu were taken without harming the fish to evaluate the morphometric variation using 8 digitized homologous landmarks for truss analysis and geometric morphometrics. Size corrected morphometric variables were analyzed using analysis of variance (ANOVA), multivariate analysis of variance (MANOVA), principal component analysis (PCA) and discriminant function analysis (DFA). Coefficients of all PCs were positively and negatively correlated to 31 significant (p 0.001) truss measurements due to variations in size and shape. Morphometric measurements lying in the head region such as head length (HL), eye diameter (ED), inter-orbital length (IOL) and snout length (SNL) contributed most to differentiate the populations in truss analysis. The ED, HL, SNL and IOL of Yamuna fish was significantly (p 0.001) smaller than the other fish populations. This could be attributed to the heavy pollution load in the Yamuna River and differences in the feeding regimes of fish. PCs and relative warps depicted differences in geometric analysis because of body shape variations among different river populations. The scatter plot in DFA revealed the presence of three distant and different phenotypic groups of W. attu among five wild river populations of fish with 70.5 and 83.9% of correct classification of fish into their original groups in truss and geometric analysis respectively. A single homogenous stock of fish was found to be in the rivers Gomti, Ganga and Hooghly because of a high level of intermixing (maximum misclassification) among the three river populations, whereas Yamuna and Pampa populations were two non-overlapping isolated groups due to negligible intermixing. These variations in the present study might be the effect of geographical isolation and river fragmentation due to the change in habitat that restricts fish movements. This is the first report on the morphometric assessment of W. attu that provides base line data for further confirmatory stock studies that would be useful for conservation and sustainable management of this vulnerable fish.