Geometric morphometrics is an efficient way to quantify biological shape variation and its covariation with other biotic or abiotic factors. The geometric information of an object is measured in a non-linear shape space after removing size, orientation, and position-related effects. This study was aimed to determine sexual dimorphism and morphological variation in body shape using landmark-based morphometrics by means of relative warp analysis. The indigenous freshwater fish Puntius sophore (Cyprinidae) was selected as the model organism for the study. Adult male and female individuals were collected during July-August 2019 (breeding season) and March–April 2019 (non-breeding season) from the ponds of Bolpur, West Bengal, India. Prior to analysis, the images were digitised using the appropriate fourteen landmarks and relative wrap analysis was performed using appropriate software. The results were then analysed, and the maximum relative displacements of adjacent landmarks were interpreted using canonical variate analysis (CVA) and principal component analysis (PCA). Significant body shape differences were found to be present in the non-breeding season and breeding season (male and female) populations of the species. Thus, geometric morphometrics can be used to understand the sexual dimorphism in natural populations of small fish species.