Morphological variations among distinctly distributed populations of Channa gachua (Hamilton, 1822) from three different geographical locations in India, viz., Gangetic Plains (GP), Western Hills and Plateau (WHP) and Eastern Himalaya (EH), were studied based on 200 specimens collected from these regions. The average total length of C. gachua was recorded as 128.5±4.0 mm, 126.3±5.5 mm and 123.1±6.9 mm from GP, WHP and EH, respectively. The analysis revealed variations in sixteen morphometric variables out of twenty measured variables among the GP and other two populations (p<0.05), except eye diameter, head width, anal fin base length and caudal fin length. However, WHP and EH populations did not show any significant difference among the measured characters. Principal component analysis (PCA) indicated that first three PCs explained 90.12% of the total variance. Linear discriminant analysis (LDA) revealed that 108 out of 200 fish samples (54.0%) were correctly classified to the actual sampling locations whereas remaining samples (46.0%) showed overlapping spatial distribution. The corrected classification rate of each population ranged from 24 to 67%. It is concluded that despite morphometric variability in head and jaws, features among GP and other two populations studied, the three must still be considered to be of the same species. The study indicates the existence of two distinct stocks of C. gachua; - one in the Gangetic Plains and another in Western Hills and Plateau and Eastern Himalayan regions.