Abstract: Fanjing Mountain is situated in Guizhou Province, southwestern China. Having the best preserved ecological system in the region, it has been designated as a national nature reserve. From 2001 to 2003, to explore the status and dynamics of the species diversity of fishes, we conducted three surveys in both the Wujiang River and the Yuanjiang River systems in the area around Fanjing Mountains. A total of 3,614 specimen were collected from 19 sites, belonging to 85 species/subspecies, 61 genera, 14 families, and 5 orders. Of these, Clarias fuscus is an introduced species while the others are indigenous. Pseudohemiculter hainanensis, Metahomaloptera omeiensis omeiensis, and Glyptothorax fukiensis fukiensis were newly recorded in this area. The fish fauna mainly comprised members of the family Cyprinidae of the order Cypriniformes, and fishes living in swift-flowing streams and small-sized species were dominant. Our study, combined with literature review, showed that indigenous fish species had decreased. Additionally, the species in Cypriniformes decreased much more than those in other orders in the area. The rapid decrease of species richness of indigenous fishes probably resulted from over-fishing and destruction of the river environment. Measures for protection of indigenous fish in this area are also discussed.