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Habitat suitability index (HSI) models are usually used to forecast habitat quality and species distributions and are used to develop biological studies, management priorities and anticipate possible changes under different management or climate change situations. This study was conducted to identify the habitat suitability index of three species namely, Capoeta buhsei, C. razii and C. alborzensis in the Kordan, Taleghan and Jajrood Rivers, respectively. At each station, environmental variables including temperature, dissolved oxygen, pH, EC, TDS and hydrological parameters such as flow velocity, depth, width, average diameter of stones and amount of phosphate, nitrate and ammonium were measured. The results showed that suitable habitats for these species are those with a high stone diameter, high temperature, low flow velocity and in areas where the width of the river is low. With respect to the abundance of fishes sampled in this study, the central and lower regions of the Jajrood and Kordan Rivers and the stations far from the dam (1 and 6) in the Taleghan River are favorable habitats for the studied Capoeta species.