We studied the biodiversity of freshwater fishes in the river systems in Qinling Ecological Protection Zone.According to the result of field survey,examination of fish specimen and references on taxonomy of fishes,the diversity of fishes species in Qinling Ecological Protection Zone was very high,with 141 species or subspecies belonging to 79 genera,16 families and 7 orders.Compared with the adjacent zones,the G-F index analysis showed that diversity of fishes in Qinling Ecological Protection Zone was ranked the first,and the index in Hanjiang was the highest in the river systems of this zone.The results of β diversity and Jaccard similarity analysis indicated that there was a significant difference in fishes distribution and composition between the south and north slope river systems.For the three river systems of south slope,the living surrounding of Nanluo and Jialing river systems was similar for fish,and there was less isolation in species and genera of fishes.While it was different for Hanjiang river system,in which there was higher isolation in species and genera of fishes.The reasons responsible for such differences were also discussed in the paper.