The ongoing explosion of nucleotide sequence data from prokaryotic and eukaryotic organisms is creating a vast information resource. Potential applications range fromunderstanding and combating human disease to characterizing naturally occurring microbial communities, whose combined biomass is the singlemost important biological force influencing global elemental cycles and the balance of atmospheric gases. Although the health sector is moving rapidly into the postgenomics era, environmental genomics, the use of genomics to address environmental issues and problems, remains in its infancy. For example, although specific nucleotide sequence information has been available for some time, whole genome sequences for environmentally relevant microorganisms are only now beginning to appear in databases. Presently, ecological studies ofmicrobial communities remain largely process-oriented. Measurable metabolic parameters, like nitrogen fixation and substrate biodegradation, are determined as a function of the whole community. The contribution of individual bacterial species to these parameters is nearly impossible to determine becausemany organisms cannot be cultivated in vitro. The use of genomics-based tools to augment these traditional methods promises to accelerate our understanding of the complexities of species diversity, population dynamics, andmetabolic pathways withinmicrobial communities in soil and water. Their use should markedly improve the reliability and accuracy of remediation activities and of predictions of adverse environmental impacts before they happen.