Morphological diversity reflects behavioral and ecological differences. Because the aquatic environment is a denser environment, the behavioral functions of fish and other aquatic organisms affect body shape. Therefore, this study was conducted to compare the morphological characteristics of pearl fish populations ( Alburnus .) in Iranian basins using geometric morphometric method. For this purpose, 487 samples of fish from the Caspian Basin (Aras, Shalmanrood, Mazoboon, Noor, Sorkhrood, Goharrood, Kaparbordrood 1, Kaparbordrood 2, Gorganrood 1, Gorganrood 2, Lamir and Hajibakandeh rivers), 170 samples from the Sistan Basin, Hamzeh river And Sistanazpashneh), 141 samples of Harirod basin (rivers of Harirod 1, Harirod 2 and Harirod canals), 51 samples of Tigris basin (Karun 1, Karun 2 and Karkheh rivers) and 5 sections of Bushehr basin (Shoor river) were sampled. The left side surface of these samples was photographed using a 14-megapixel Canon camera, and then 13 landmarks were digitized using tpsDig2 software. Data obtained from Procrustes analysis were analyzed by multivariate statistical methods of PCA, CVA and cluster analysis. Comparison of geometric morphometry showed that there was no significant difference between the populations of different basi however, there is a significant difference between Sistan and Bushehr. The main differences observed along the PC and CV axes were head size and shape, change in mouth position, body height, fin position, and tail stem length.