Seven bacteria strains were isolated from the samples of an acid mine drainage stream in the Shizishan sulfide mine, Tongling, by using the overlay technique with four selective media of YE, Feo, FeSo and FeTo. The 16S rRNA gene sequences were amplified from total DNA of bacteria strains and were then sequenced and analyzed．The phylogenetic tree analysis with 16S rRNA gene sequences of isolated bacteria strains was carried out. The results show that every isolated bacteria strain can be divided into three microbial communities, namely heterotrophic acidophiles, autotrophic acidophiles and moderately acidophilic iron_oxidizing bacteria. The function of heterotrophic acidophiles lies in the dissimilatory ferric iron reduction and the creation of an oligotrophic environment. Autotrophic acidophiles can oxidize iron and sulfur elements in acid mine drainage, being producers of the acid mine drainage ecological system. Moderately acidophilic iron_oxidizing bacteria can oxidize ferrous iron and generate some insoluble minerals to realize the dynamic balance of iron element between the acid mine drainage and the sediments.