The main purpose of this study was to investigate the morphological changes and body shape variations of the Zagros Tooth-carp Aphanius vladykovi populations in six water bodies located in Chaharmahal and Bakhtiari province, Iran. For this purpose, 240 specimens were collected from the Choghakhor and Gandoman wetlands, the Shalamzar, Balagholi, and Brovi springs, and the Beheshtabad River. Twelve landmark points were digitized on the right side of the fish. Statistical analyses including Principal Component Analysis (PCA), Discriminant Function Analysis (DFA), and Cluster Analysis (CA) were performed using TPS package, SYSTAT 9, and PAST Software. Discriminant function analysis revealed that female fish in different localities show more pronounced body shape differences compared to males from different localities (p <0.001). In addition, in clustering analysis performed among males and among females, two clusters were resolved, which were fairly similar for males and females. These differences might be attributed to the morphological adaptation of the Zagros Tooth-carp to their habitats but a clear inference on the observed morphological divergence will be possible with more genetic, ecological, and experimental evidence.