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. In this study, morphological variation of three species of Squalius in Iranian basins was studied. For this purpose, 709 specimens were captured from the Caspian Sea, the Urmia Lake, the Namak Lake and the Tigris basin. After anesthetizing in clove oil solution and fixing in 10% neutralized formalin, specimens were transferred to the Isfahan University of Technology Ichthyology Museum (IUT-IM) for further studies. In the laboratory, some 14 meristic characters were counted under a streomicroscope. Also, images were analyzed with ImageJ software and 19 morphometric characteristics were measured. In addition, 13 landmarks were defined and digitized on images taken in tpsDig2 software in order to extract geometric morphometric data. Kolmogorov-Smirnov, Kruskal-Wallis, ANOVA, Duncan test, PCA, CVA and cluster analysis methods were used to analyze the differences among the populations. The results of PCA and CVA meristic and morphometric analyses showed no significant differences among the studied populations. The populations of the species studied were significantly different in 11 meristic and 15 morphometric characteristics. Also, the major differences observed in the results of geometric morphometric analysis were related to the position of the pectoral fin, body and head depth. In general, the studied populations highly overlapped, and we suggest that the populations of genus Squalius should be further studied by molecular methods.