The interaction between mankind and the environment has led to the need for a series of programs to reverse or remediate environmental damage. While the building of canals, roads, and buildings; the manufacture of chemicals and products to support economies worldwide; and the mining of natural resources have benefited mankind, these activities have also caused serious, potentially long-term impacts on numerous natural environments. For example, these impacts have included contamination of surface and ground water, soils, and sediments; stripping of surface soil layers; and generation of hazardous waste sites. Programs to address these issues include remediation programs targeted at hazardous waste sites and toxicity identification and reduction for toxic effluents. This workshop, in general, and this chapter, in particular, focus on the application of genomic technologies to contaminants in the environment. Thus, this chapter is primarily concerned with application of genomics to sites requiring remediation due to the presence of contaminants.