Abstract:The composition of microbial communities in five waste mining water samples (from Tong lvshan copper mine, Hubei province, and Zhong tiaoshan copper mine, Shanxi province) were studied, using culture-independent 16S rDNA based cloning approach-restriction fragment length polymorphism (RFLP) analysis method. Phylogenetic analysis revealed that the bacteria in these five samples fell into 4 major groups: Proteobacteria, Nitrospira, Firmicutes and Bacteroidetes. Archaea were only detected in samples from Tong lvshan copper mine. Thermoplasma and Ferroplasma lineages were detected abundantly in these two samples. Meanwhile, the results of Principal Component Analysis (PCA) 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 among water samples in this study.