Abstract: Periphyton acts as the primary basal food resource of indigenous and unique fishes in the cross-border rivers of Xinjiang Uygur Autonomous Region. Research of the periphyton in this region is still limited. To investigate the community structure of periphyton, samples were collected in July, August and October 2012 from Irtysh River located in Xinjiang Uygur Autonomous Region. Our study indicated that the periphyton assemblage was composed of 178 species in total, belonging to seven taxonomic groups. Bacillariophyta showed the highest number of taxa (92), followed by Chlorophyta (49), Cyanophyta (20), Euglenophyta (5), Cryptophyta (3), Chrysophyta (2) and Pyrrophyta (1). Species number of periphyton showed significantly differences in different seasons (P 0.01). Bacillariophyta was predominant in species composition, especially N. halophila, Fragilaria capucina, C. perpusilla and Phormidium corium Gom. The average cell density and biomass of periphyton were 1105.5 ind./m2 and 2692.0 mg/m2, respectively. Although seasonal and spatial distribution of density and biomass were not significant difference, the overall trend of spatial distribution showed that the density and biomass in lower-middle region were higher than those in upper region. Average values of diversity indices (D, H'), evenness (J) and abundance (Dm) of periphyton were 0.38, 3.04, 0.66 and 2.55, respectively. The water quality of Irtysh River has mild contamination based on the diversity index and phytoplankton abundance.