Two acid mine drainage (AMD) samples TS and WK, which were from the Dachang metals-rich mine in Guangxi province, China, were studied using PCR-based cloning approach. A total of 44 operational taxonomic units (OTUs) were obtained from the two AMD samples. However, only three OTUs (GXDC-9, GXDC-19 and GXDC-50) detected in sample TS can also be observed in sample WK. Phylogenetic analysis revealed that the bacteria in the two samples fell into four putative divisions, which were Nitrospira, Alphaproteobacteria, Gamaproteobacteria, and Acidobacteria. Organisms of genuses Acidithiobacillus and Leptospirillum, which were in gamaproteobacteria class and Nitrospira family, were dominant in two samples, respectively. In sample TS, which was characterized by low pH, high sulfate, high iron, and high arsenide, two species (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans) constituted 98.22% of the entire microbial community. Compared with sample TS, the microbial community in sample WK was more diversified according to the observation. Interestedly, the Legionella species, which was rarely observed in the low-pH environment, was detected in sample WK. This work helps us to further understand the diversity of microbial community living in extreme acid mine drainages with unique geochemistry and the tolerance capability of acidophiles to heavy metal.