Species population structure and composition are components of essential biodiversity variables (EBVs) to measure change in global freshwater diversity. Multiple stressors affect the population structure of coldwater fishes in the Indian Himalayan Region (IHR). In this study, 463 individuals of snow trout, Schizothorax richardsonii were collected from 14 locations on seven rivers of IHR (Satlej, Chenab, Beas and Ravi rivers of Indus basin, and Bhagirathi, Alaknanda and Kosi rivers of Ganges basin) to assess the inter and intra-basin population-level shape variation through landmark-based “geometric morphometrics”. Procrustes ANOVA on the superimposed shape coordinates revealed significant relationship (F = 4.51, p < 0.05) among groups. Principal component analysis (PCA) accounted for 42.37% of the total variance (22.69% for PC1, 19.68% for PC2), indicating overlapping among populations. Canonical variate analysis (CVA) accounted for 66.71% of the total variance (37.07% for CV1 and 29.64% for CV2), indicating non-overlapping between basins and within Ganges basin, and overlapping within Indus basin. Pair-wise distances extracted from PERMANOVA also found to be non-significant (p > 0.05) between Satlej, Chenab, Beas and Ravi rivers, indicating overlapping of samples within the Indus basin, and significant (p < 0.05) between rivers of Indus basin, Alaknanda, Bhagirathi and Kosi river systems, indicating non-overlapping of specimens between these rivers. Overall, results of multivariate analysis indicated four heterogeneous populations of snow trout in the selected rivers based on their shape: 1. Indus basin comprising of Satlej, Chenab, Beas and Ravi rivers, 2. Bhagirathi River, 3. Alaknanda River and 4. Kosi River. This study will be useful in stock identification, and provide a key to climate change and demographic research for developing sustainable management strategies to conserve this threatened species.