The members of the Chondrostoma are very similar to each other, which is a limiting factor for identifying the species of this genus and studying the phylogenetic relationships of this genus. Little systematic information is available, and their identification is often based on uncertain characters, and sometimes their identification is impossible. Comparison of morphological structures is a key element in evolutionary biology, which is used both in archeology and understanding of the diversity of organisms. The aim of this study was to investigate and study Chondrostoma species in order to identify their dignostic bony characteristics. Therefore, eight populations of this species were collected from Isfahan, Tigris, Bushehr, Fars, and Caspian basins and transferred to the laboratory. After clearing and staining with Alcian blue and Alizarin red, they were photographed using a stereomicroscope and a digital camera. In the jawbone, maxillary mid-lateral assending processin Chondrostoma regium is almost flat and pointed on the left, in Chondrostoma cyri round or crested and in Chondrostoma orientale is almost flat. In the mandibular, the dorsal part of the articular in C. regium is almost stright, but in C. cyri and C. orientale is convex. In the opercular series of the upper edge at the point of attachment to the hyomandibular in C. regium is pointed, in C. cyri rounded and in C. orientale is slightly pointed (between the two previous modes). The dorsal arm of ceratobranchial at the end of the pharyngeal teeth in C. regium is pointed, in C. cyri rounded and in C. orientale between the two previous modes. In the caudal skeleton, the rudimentary neural arch in C. regium is short and almost pointed, in C. cyri is long and wide and in C. orientale is relatively long and quite pointed. In the neurocranium, the posterior pharyngeal process in C. regium is in the middle, narrow, and slightly flattened, in C. cyri , it is broad from the beginning to the end and in C. orientale is widened and flatend from the beginning to the end. In the hyiod arch,the basihyal in C. regium is wide and short, in C. cyri is slim and elongated and in C. orientale is slim and short. The skeletal structure of this genus also showed differences in the shape of the maxilla and premaxilla, quadrate, symplectic, parasphenoid, basioccipital and urohyal bones with other carps, which these cases can be considered as recognizable osteological characteristics of this genus. Keywords : Chondrostoma , Bone structure, Taxonomy