An investigation was carried out on the benthic algal communities at 22 sites in the Jinping reach of Yalong River and its main tributaries in May and November 2004, aimed to study the relationships between benthic algal distribution and environmental variables. A total of 150 taxa (mostly to species level) in 37 genera were observed, which belonged to Bacillariophyta, Chlorophyta and Cyanophyta. Diatoms comprised 96.5% of the total taxa. Achnanthes linearis and Achnanthes deflexa were the most abundant species, and the relative abundances were 35.3% and 11.0% of the total abundance, respectively. In May and November, Nitzschia dissipata and Gomphonema parvulum were the dominant species in Jinping reach of Yalong River, while Achnanthes linearis, Cocconeis placentula and Achnanthes deflexa dominated in its tributaries. Based on the species composition and their relative abundance, detrended correspondence analysis (DCA) showed that sites belonging to Yalong River and its tributaries were well separated on DCA axis 1. This may be explained by the special habitats of Yalong River like high velocity, wide channel width. Canonical correspondence analysis (CCA) on the relationships between benthic algal community structure and environmental variables indicated that in May, TP was the main environmental variable affecting the benthic algal distribution, while in November, NH4-N and elevation were the main ones.