Truss-based morphometric analysis was used to examine phenotypic plasticity of Barilius vagra (Hamilton, 1822) inhabiting the tributaries of the Alaknanda (Ganga River basin) and Chenab (Indus River basin), two geographically distinct river basins in the Indian Himalaya. Fourteen landmarks were connected to generate a truss network of 90 parameters on the body of fish. Eighty morphometric traits out of ninety morphometric measurements explained statistically significant difference among six sampling locations of Barilius vagra from streams in the Alaknanda and Chenab basins. Discriminant function analysis revealed 82% of Barilius vagra specimens originally classified into their own groups. 95% of the variance was explained by 13 principal components. Morphometric characters (1–6, 1–13, 2–5, 2–6, 2–14, 3–6, 4–6, 4–14, 6–12, 7–8, 7–9, 10–11, and 13–14) contributed greatly in differentiation of B. vagra populations from different river basins. The Alaknanda basin reflected some mixing within populations, which may be due to common environmental conditions and fish migration in these streams. This study will be helpful in framing site-specific conservation and management strategies, such as net mesh size selection, avoiding overexploitation, stock augmentation and food availability for different fish populations.