Several species of Cobitis have been reported within Iran, but only four are recognizedas valid. The geographical distribution and genetic diversity of these species are notwell-known. Two new populations of C. saniae and C. avicennae were reported hereinbased on their morphological and phylogenetic characters from the Mahabad River, atributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkhehdrainage, respectively. The genetic diversity and genetic structure of populations of C.saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of themitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan,and Georgia were used. A moderate to high level haplotype diversity and low nucleo-tide diversity were found in most of the populations of all three species. The AMOVAtest and pairwise FST comparison revealed significant genetic structure and genetic dis-tance between the Urmia Lake basin and other C. saniae populations. The results high-light the importance of conserving these species and their habitats, particularly in theUrmia Lake basin, where significant genetic differentiation was observed
