The composition of microbial communities in five acid mine water samples were studied, using culture-independent 16S rDNA based cloning and restriction fragment length polymorphism (RFLP) analysis. Phylogenetic analysis revealed that the bacteria in these five samples fell into 4 major groups: Proteobacteria, Nitrospira, Firmicutes and Bacteroidetes. Proteobacteria organisms such as A. ferrooxidans appeared in samples SX3, K1 and K2, but was scarce in samples SX1 and SX2; Nitrospira organisms Leptospirillum ferrooxidans, Leptospirillum ferriphilum and Leptospirillum group III, were prevalent in samples SX1, K1 and K2, but with fewer in samples SX2 and SX3. Archaea were only detected in samples K1 and K2 from the Tong shankou copper mine. Thermoplasma and Ferroplasma lineages were detected abundantly in these two samples. Meanwhile, the results of Principal Component Analysis (PCA) based on the percentages of OTUs and data of biogeochemical parameters, revealed that biogeochemical properties affected the diversity of microbial communities in mine water. The pH, temperature and different concentrations of elements such as S, Ni, Co and Cu seemed to be key factors resulting in the diverse distribution of microbes.