Oxynemacheilus bergianus is found in several inland water basins of Iran. Due to its wide distribution, this study was conducted to investigate its morphological variation in basins of Caspian Sea and Namak Lake of Iran using geometric morphometric technique. For this purpose, a total of 115 specimens from five river (Sefid and Ghezel Ozan (Caspian Sea basin), Jajrood, Kordan, Qom (Namak Lake basin)) were caught and compared using geometric morphometric method. The results indicated a completely different body shape patterns in the studied populations. The results also showed a significant difference between the body shape of the studied and groups the most differences were related to tail length and depth, body depth, head length and position of the dorsal, anal and pectoral fins. The observed shape patterns can indicate habitat-dependent morphological separation and geographical distances that the geometric morphometric method was highly capable of separating morphological features due to their high capability.