The morphological variation of the endangered catfish Rita rita was studied based on meristic, length–weight relationship (LWR), traditional (TRA) and truss (TRU) distance based morphometric analysis of 200 juveniles collected from the Old Brahmaputra, Jamuna, Meghna and Kangsa rivers. Data were subjected to Kruskal–Wallis test for meristic counts, t test for LWR, univariate ANOVA, multivariate discriminant function analysis and canonical analysis (CA) both for TRA and TRU morphometric characters to discriminate the populations. Kruskal–Wallis test denoted that only one (caudal fin rays) out of six meristic counts was significantly (p < .05) variable among the stocks. One sample t test clarified that all parameters of LWR were significantly (p < .05) differentiated in all stocks. Univariate ANOVA revealed significant (p < .001, p < .01, and p < .05) differences among the four stocks in 14 of 15 standardized TRA traits and 17 of 25 TRU distances, respectively. The first discriminant function (DF1) explained 59.4% and 68.0% of total variance, while 30.6% and 23.1% by DF2, 10.0% and 8.9% by DF3 for TRA and TRU features, respectively among the stocks. CA showed a clear separation of the stocks both for TRA and TRU measurements. The overall random assignment of individuals into their original groups was high as 78.5% for TRA and 78.0% for TRU characters, respectively, indicating that all the four stocks are highly divergent from each other. The results exposed existence of four distinct phenotypic stocks of R. rita in the tested rivers.