Microbial bioremediation serves as an alternative and effective strategy to remove toxic contaminants from a polluted environment. It could be achieved through the interaction of microbes with the toxic contaminants, which leads to immobilization, compartmentalization, and concentration of pollutants rather than their degradation and elimination from the environment. Bioremediation of the contaminated sites employing indigenous microbes is highly advantageous as it is ideally adapted to the environmental conditions prevailing at the site to be remediated. Traditional culture-based approaches have provided only limited information on the metabolic potential and the functional activity of the indigenous microbial communities living in the contaminated environment. Recent development of metagenomic approaches and advancement of high-throughput DNA sequencing technology provides insight into the total microbial community and in-depth knowledge of the metabolic capabilities of the indigenous microbial community prevailing in contaminated sites. Metagenomic approaches could address environmental issues by exploring the phenomenal resources of the uncultivable microorganisms. The present chapter describes the application of metagenomic strategies for better understanding of the indigenous microbial communities and their functional abilities to clean up toxic contaminants from polluted sites, which will provide new perspectives on environmental management. © 2014 Elsevier Inc. All rights reserved.