River originates from alpine springs on the slopes of the Tanggula Mountain in Qinghai-Tibet Plateau, and the species and distribution of fishes are very special in the river. To understand the present composition and distribution of fishes in this water system, a comprehensive survey was carried out in Yunnan section of Lancang River and its affiliated lake, Erhai Lake. Fifty two sampling sites were set up based on the different elevation and multiple habitatation. In the 4 787 fish samples collected, five orders, 14 families, 80 species of aboriginal fishes were identified, with another 59 species recorded in references. All the fishes, consisting of six orders, 18 families, are composed of fishes from two regions: Xikang-Tibetan Sub-region belonging to West China Region and Nukiang-Lancang Subregion belonging to South China Region. In addition, 21 species of exotic fishes were collected. The differences in horizontal and vertical distribution of aboriginal fish are obvious. The horizontal distribution shows an obvious diversity and regional variety. The distribution of fish in Lancang River was influenced by altitude and climate. Many groups of fish have a certain distribution range. The Tetraodontiformesand some species of the Cypriniformes are limited to low elevation regions in the tropics. The distribution of the ake up a large proportion in Lancang River shows a gradual of different groups with the rise of altitude. Compared with the historical data, the current species number of aboriginal fish in some sections of Lancang River has decreased obviously. Environmental stress caused by river construction, over-fishing, pollution and exotic fish is external impact factors for fishes in Lancang River. Relevant departments should adopt various measures to tackle the problem such as establishing nature reserves, promoting artificial enhancement and releasing, setting up eco-environment monitoring system, improving aquatic living resources and environment administrative systems.