An understanding of the stock is a basic requirement for the management of the fishery resources. The endangered mahseer, Tor putitora (Hamilton, 1822) is a commercially important fish distributed extensively in the foothills of Himalayas. Box plots and multivariate statistical tools like Principal Component Analysis (PCA) and Discriminant Function Analysis (DFA) were used to delineate the stocks of T. putitora from two Indian rivers, Yamuna and Satluj using 6 meristic and 24 morphometric characteristics. A comparison of the morphometric and meristic characters using box plots revealed variations in eye diameter (ED), length of rostral barbel (LRB), standard length (SL), pre-anal distance (PAD), distance between pectoral and pelvic fin (DPP), distance between pelvic and anal fin (DPA), length of dorsal fin (LDF), length of pectoral fin (LpecF), length of pelvic fin (LpecF) and length of caudal fin (LCF) for distinguishing populations from these two rivers. Upon PCA, the first three principal components accounted for 69.66% of total variance in head parameters whereas for total length, the first 5 principal components accounted for 73.23% of total variance. For meristic characters, the first two PCs explained 75.65% of the total variance. The step-wise DFA retained only one function for morphometric as well as meristic characters explaining 100% of the variance. The Wilks’ lambda tests for morphometric and meristic data indicated differences between the populations of T. putitora from both the rivers.