The genus Chondrostoma (Leuciscidae: Leuciscinae), composed of small to medium-sized fish with a scraper feeding characteristic, is distributed in the West and Middle East, Caucasus, Europe and Northern Mediterranean drainages. This genus spreads across Anatolia and Thrace, with the exception of Göksu and Eşen rivers in Turkey’s Mediterranean basin. It is also difficult to understand the systematics of Chondrostoma, which is complicated morphologically. Therefore, in this study, an identification key was made by evaluating external morphology, osteology (some jaw bones and 5th ceratobrachial) and molecular features together. A total of 13 valid species have been so far recorded from Turkish inland waters, among which are C. beysehirense, C. ceyhanensis, C. colchicum, C. cyri, C. holmwoodii, C. kinzelbachi, C. meandrense, C. nasus, C. regium, C. smyrnae, C. toros, C. turnai and C. vardarense. Our molecular data showed that C. angorense (Kızılırmak and Sakarya rivers) is a synonym of C. colchicum (Çoruh and Yeşilırmak rivers). In addition, C. angorense was morphologically similar to C. colchicum. Therefore, we explored the systematic position of C. vardarense (from Meriç River) and C. nasus (from Simav River) in this study.