To evaluate the feasibility of using the shape of neurocranium in identifying the species of the genus Cyprinion by geometric morphometric technique, 30 specimens of five Iranian species were caught. For this purpose, 17 homologues landmark points were defined and digitized on 2D pictures taken from the dorsal view of their neurocranium. The data (coordinates of the landmarks) were analyzed according to Principal Component Analysis (PCA), Canonical Variate Analysis (CVA) and Cluster Analysis (CA) using MorphoJ and PAST soft wares. The statistical analyses could discriminate five species according to the shape of neurocranium. The key characters that can be used to describe species are the following: C. kais bears the least cranial width at lateral ethmoid region, the least narrowing at mediolateral neurocranium and the least distance between anterior to posterior connection point of palatines. C. macrostomum possesses the least supraethmoid width and there is a notch in its anterior most border and also has the most distance between the anterior to posterior connection points of the palatines. C. milesi has the narrowest and more elongated neurocranium among Iranian Cyprinion genera, and has the narrowest neurocranium in the mediolateral of the neurocranium. In C. tenuiradius, the neurocranium is wide at pterotic region, decreases in mediolateral regions and then increases at lateral ethmoid region. Finally C. watsoni has the widest and shortest supraethmoid among Iranian Cyprinion fishes.