This study was conducted to investigate the interspecies morphological variation of Sabzug (Cyprinion watsoni) in response to environmental factors using geometric morphometrics method in Southern and Southeastern Iran. Hence, nine populations including 270 specimens of Sabzug were collected from four Southern and Southeastern basins of Iran during summer 2012 using electrofishing. The specimens were anesthetized in clove solution 1gl-1, fixed into 4% formalin and then transported to the laboratory for further examinations. The left view of specimens was photographed and fifteen landmark-points were defined and digitized on 2D images using tpsDig2 software. The shape data were analyzed based on Principal Component Analysis (PCA), Canonical Variate Analysis (CVA) and Cluster Analysis (CA). The results revealed a significant difference between populations in terms of body shape (P<0.01). Also, the Bastak population was considerably separated from all other populations. The results can be summarized as: the Sarze, Ilood, Jegin and Sarbaz populations had more body height, in Ilood, Kash, Mashkil, HalilRood and Jegin the head was longer and in Ilood, HalilRood and Jegin the head height were more than other populations. The Bastak population was differentiated due to possessing the least body height, longer head, more up-warded mouth and less caudal peduncle length than others. These results revealed some morphological responses of Sabzug to environmental selective pressures, which can be used in taxonomic and systematic study of the genus Cyprinion.