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Garra rufa is one of the 73 Garra species of the family Cyprinidae. Scales are used more commonly than any other structure in population dynamic studies, because of their transparency, ease of sampling, and the minimal in-juries caused to the fish during their removal. To discriminate fish from different rivers including Bashar, Behbahan, Gerdab, Kheirabad, Kooshk-e-Bahram, Mazoo, Palangan, Sendegan, Shoor-Abad, and Sirvan Rivers using geometric morphometric analyses of the scale shape, landmark based geometric morphometrics method was used. Seven landmark points were depicted on each scale using the software TpsDig2. After procrustes analyses, landmark data were exposed to principle component analysis (PCA), CVA, and cluster analyses using the past software. The results showed that th-ere were significant scale shape differences among some populations, but most of the samples showed overlapping sh-ape distribution and could not be separated robustly. Among the samples which were analyzed, only the Sendegan and Gerdab river samples did not show significant difference in scale shape compared to all other samples.

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The cave barb habitat is located in a Karst formation along the Sezar River. The springs on the walls of the Sezar River valley may provide a means for fish in surface waters to penetrate into the underground waters. These observations propose the probability for a migratory relationship between Garra gymnothorax in the Sezar River and the cave barbs (Garra typhlops and Garra lorestanensis). In addition, a variety of different body shapes including fusiform and slender body forms are observed among the cave fish. This phenotypical variation may be a sign of an unknown genetic diversity or could be attributed to the variable environmental conditions in different parts of the subterranean habitat. To clarify the situation, we used the sequences of mtDNA cytochrome oxidase subunit I and next generation sequencing method. The results showed that the fusiform and slender body shapes of G. typhlops and G. lorestanensis were not different with regard to their mtDNA and genomic compositions. Moreover, the analysis of the genomic their mtDNA and genomic compositions. Moreover, the analysis of the genomic showed that a limited level of gene flow (less than 3%) from G. gymnothorax probably existed in G. thyphlops. The low level of gene flow may be related to the lower fitness and adaptability of the surface dwelling fish to the subterranean life conditions.