The negative impact of acid mine drainage (AMD) on public and environmental health by degrading the aquatic and terrestrial ecosystem with a drastic decrease in pH and elevated levels of toxic heavy metals, metalloids and radionuclides necessitate the development of environmentally sustainable technologies to remediate AMD. The development of appropriate strategies for controlling and/or abating the detrimental effects of AMD in natural and mining environments primarily depends on the diversity and compositions of the local acidophilic microbial communities (those which can grow at pH <= 3) which catalyze the reactions of AMD by production of sulfuric acid and ferric iron. Robust method(s) to track the AMD-promoting microbial communities will not only provide information about their ecophysiological role in extreme environments but also help sustain the reliability of remediation technologies. This paper provides an overview on the phylogenetic diversity of prokaryotes present in AMD-impacted environments, and different molecular methods that have been used to track the diversity of these acidophiles. Additionally, the high-throughput methods (metagenomics, metaproteomics and microarrays) that link prokaryotic phylogeny to their function in AMD systems are also discussed. (C) 2011 Elsevier Ltd. All rights reserved.