Environmental pollution is one of the most serious global challenges. Wild-type organisms have a slower degradation rate of hazardous materials. Currently, advanced molecular biology tools along with conventional approaches allow us to rapidly degrade or accumulate hazardous materials from environments. This can help modify microorganisms to gain the ability to sense and degrade hazardous chemicals from contaminated sites, in turn, allowing us to grow vegetation and improve crop productivity. In this chapter, conventional and advanced molecular biology tools for the removal and detoxification of contaminants from soil and water to improve environmental conditions are highlighted. Environmental pollution represents an obstacle to the economical exploitation of coal deposits. In industrialized countries, the rules for protection of the environment are stricter than in developing countries. Thus, to get a license to open mines involves lengthy procedures which in turn cause delay. Indian authorities have also started to put stringent conditions in place regarding environmental pollution. Consequently, ecological problems can be totally prevented, but such measures are costly.