Pyrite tailings can cause serious pollution to the surface water as the strong acidity, high iron and sulfate concentration in the leachate. The bacterial communities of pyrite tailings polluted area were still unclear which could restrict the recognition of the pyrite tailings pollution effect and further impede the development of microbial or ecology treatment technologies. In this study, the bacterial communities in the polluted area of pyrite tailings, from the upstream, pollutant source, and to the downstream, were analyzed with Illumina HiSeq sequencing. Results showed that Acinetobacter and Flavobacterium were abundant in the water and sediment of upstream and downstream while Bacteroides, Lactobacillus, and Akkermansia were abundant in the pollutant source. Sulfur-metabolizing or iron-metabolizing bacteria extensively existed in the polluted area in which Acidiferrobacter, Ferrithrix, and Desulfovibrio played crucial roles on the whole communities. Sulfur-metabolizing bacteria (e.g. Thiomonas, Sulfurospirillum, and Desulfobulbus) and iron-metabolizing bacteria (e.g. Ferrimicrobium, Ferrithrix, and Ferrovum) were introduced to the river polluted by pyrite tailings. Pyrite tailings can remarkably change the physicochemical characteristics and bacterial communities of river water and sediment.