Scale morphology and its structural details were studied with morphometry, geometric morphometrics, and scanning electron microscopy in five Iranian Aphanius species and examined comparatively with molecular phylogeny. Scales were cycloid and circular in A. farsicus Teimori, Esmaeili & Reichenbacher and A. vladykovi Coad, cycloid and polygonal in A. isfahanensis Hrbek, Keivany & Coad and A. sophiae (Heckel), and were spined and polygonal in A. dispar Rüppell. Univariate analysis indicated that the relative length of anterior margin of radii played a significant role in the separation of some species studied (P < 0.05). Canonical Variates Analysis (CVA) based on seven landmarks showed clear separation between the Iranian inland and inland-related Aphanius species (IIRAS) group (four species) and the brackish water species (A. dispar). The lepidonts were conical in the IIRAS group with the exception of A. isfahanensis (rounded) and were rounded in A. dispar. Based on the basal position of the brackish water Aphanius species in the phylogenetic trees of the genus Aphanius, it can be assumed that the presence of rounded lepidonts was a primary state in their scales or is the result of convergent evolution. Also, the polygonal state in the scales of Aphanius species was a primitive shared character state.