One of the largest, original open-cast copper mines in China provides an excellent opportunity to investigate microbial community structure in extreme environments. Microbial diversity of acid mine drainage and sediment samples from three sites within the mine were analyzed by 16S rRNA gene library and restriction fragment length polymorphism (RFLP) analysis. A total of 40 unique 16S rRNA genes, screened from 558 clones, were obtained from all sites. The sequenced clones fell into seven phylogenetic divisions. The majority of the clones were affiliated with the γ-Proteobacteria, α-Proteobacteria and Nitrospira. At all sites examined, the proportion of Acidithiobacillus ferrooxidans in the acid mine drainage is greater than that in the sediment. In contrast, the proportion of Acidiphilium is greater in the sediment than that in the acid mine drainage. This may be due to the anaerobic environment within the sediment, which inhibited aerobic bacteria, such as A. ferrooxidans. However, Acidiphilium, a heterotrophic bacterium, is able to catalyze the dissimilatory reduction of ferric iron to ferrous even in the presence of small amounts of oxygen.