Study of the diversity and genetic structure of various fish species are one of the most basic indexes for preservation and restoration of their reserves. the aim of this study is to review taxonomy of a genus of hillstream loaches paraschistura, by molecular methods using gene sequences obtained by cytochrome oxidase gen in the south of Iran. For this purpose, an adult sample of any species which include: 7 specimens P.bamporensis, 3specimens P. sargadensis, 4specimens P.hormozensis, and 5specimens Parascshistura sp. was collected from south of Iran. DNA of these samples was extracted by genomic kit and FCOI20' primer, and was multiplied during PCR process and sequencing after electrophoresis. in order to study phylogenetic relations of COI gene of above mentioned fishes MEGA6 software was used .the results of the study showed that samples of paraschistura genus are placed in 4 clades. Samples of p.bampurensis from different locations with evolutionary distance (0.005-0.128) and P. sargadensis are located in one clade close to each other. samples of p.hormozensis with evolutionary distances (0.042) are located on separate clades. accordingly P. abdolii, P. naumani AND P. delvarii with evolutionary distances (0.042-0.206) and Parascshistura sp With an evolutionary distance(0.030-0.185) are located on separate clades.Considering the distance of location from each other and also study of morphological traits, molecular results were consistent with morphological traits. Phylogenetic tree analysis in this study shows that morphologic characters together with molecular identification are needed to support recognition of species.