The Tarim River system lies in the border of QinghaiTibetan plateau, it is typical arid desert climate, and the species and distribution of aboriginal fish are very special. To master the compositon and distribution of aboriginal fish in this water system, the authors carried out a comprehensive survey on the seven water systems of Tarim River. The researchers set up 200 collection points, collected 3000 fish samples, and identified 1 order, 2 families 5 genera, 12 species, which all belong to Schizothorax and Triplophysa of central Asian mountain complex. The differences in horizontal and vertical distribution of aboriginal fish are obvious. The horizontal distribution shows an obvious diversity and regional variety, and the vertical distribution shows an obvious zonal variety. The first grade national protected animal Aspiorhynchus laticeps only distributs below 1 500 m altitude, Schizothorax maily inhabits at 1 300 - 2 700 m altitude, Gymnodiptychus mainly inhabits at 1 500- 2 900 m altitude, and Diptychus mainly inhabits at 2 700-3 700 m altitude. Triplophysa at the similar altitude of Schizothorax, but up to 3 700 m. The largescale and large spatial distribution pattern of aborginal fish in Tarim River shows a trend toward narrow, the habitats of Aspiorhynchus laticeps become islandized highly. This article reports the situation of aboriginal fish in Tarim River system comprehensively and systematically for the first time, it provides full and accurate information for comprehensive management of Tarim River system and protection of aboriginal fish.