Mine water is an example of an extreme environment that contains a large number of diverse and specific bacteria. It is imperative to gain an understanding of these bacterial communities in order to develop effective strategies for the bioremediation of polluted aquatic systems. In this study, the high-throughput sequencing approach was used to characterize the bacterial communities in two different mine waters of South Africa: vanadium and gold mine water. Over 2629 operational taxonomic units (OTUs) were recovered from 15,802 reads of the 16S ribosomal RNA (rRNA) gene. They represented 8 phyla, 43 orders, 84 families and 105 genera. Proteobacteria and unclassified bacterial sequences were the most dominant. Apart from these, Firmicutes, Bacteroidetes, Actinobacteria, Candidate phylum OD1, Cyanobacteria, Verrucomicrobia and Deinococcus-Thermus were the recovered phyla, although their relative abundance differed between both the mine-water samples. Yet, diversity indices suggested that the bacterial communities inhabiting the vanadium mine water were more diverse than those in gold mine water. Interestingly, substantial percentages of the reads from either sample (58 % in vanadium and 17 % in gold mine water) could not be assigned to any phylum and remained unclassified, suggesting hitherto unidentified populations, and vast untapped microbial diversity. Overall, the results of this study exhibited bacterial community structures with high diversity in mine water, which can be explored further for their role in bioremediation and environmental management.