Heavy metal-contaminated regions are common across the planet. The treatment of such regions (especially those co-contaminated with other toxic substances), remains one of the most costly environmental challenges currently faced by many countries. It appears that the employment of microorganisms in biotransformation of heavy metals is a good solution to this problem, however a key step in the waste management technologies is the understanding of the mechanism of heavy metals resistance, metabolism and transformation. Recent advances in genomics, metagenomics and metatranscriptomics increased their role in identifying traits that may maximize the benefits of heavy metals bioremediation technologies.