The reduction of perchlorate to chlorite, the first enzymatic step in the bacterial reduction of perchlorate, is catalyzed by perchlorate reductase. The genes encoding perchlorate reductase (pcrABCD) in two Dechloromonas species were characterized. Sequence analysis of the pcrAB gene products revealed similarity to ␣-and -subunits of microbial nitrate reductase, selenate reductase, dimethyl sulfide dehydrogenase, ethylbenzene dehydrogenase, and chlorate reductase, all of which are type II members of the microbial dimethyl sulfoxide (DMSO) reductase family. The pcrC gene product was similar to a c-type cytochrome, while the pcrD gene product exhibited similarity to molybdenum chaperone proteins of the DMSO reductase family members mentioned above. Expression analysis of the pcrA gene from Dechloromonas agitata indicated that transcription occurred only under anaerobic (per)chlorate-reducing conditions. The presence of oxygen completely inhibited pcrA expression regardless of the presence of perchlorate, chlorate, or nitrate. Deletion of the pcrA gene in Dechloromonas aromatica abolished growth in both perchlorate and chlorate but not growth in nitrate, indicating that the pcrABCD genes play a functional role in perchlorate reduction separate from nitrate reduction. Phylogenetic analysis of PcrA and other ␣-subunits of the DMSO reductase family indicated that perchlorate reductase forms a monophyletic group separate from chlorate reductase of Ideonella dechloratans. The separation of perchlorate reductase as an activity distinct from chlorate reductase was further supported by DNA hybridization analysis of (per)chlorate-and chlorate-reducing strains using the pcrA gene as a probe.Ammonium perchlorate (NH 4 ClO 4 ), a common component of solid rocket fuel, is a widespread environmental contaminant in water systems in the United States (9, 25). While attempts at implementing regulatory standards have created discord between the Environmental Protection Agency and other federal agencies (9, 26), perchlorate remains a health issue due to its effects on the thyroid gland (34). Based on the chemical properties of perchlorate, remediation efforts have focused primarily on dissimilatory perchlorate-reducing bacteria (DPRB). Despite the isolation of over 50 perchlorate-reducing strains (6,(8)(9)(10)33), our knowledge of the metabolic pathway involved is rudimentary.Chlorite dismutase and perchlorate reductase are the only enzymes in the perchlorate reduction pathway that have been isolated and characterized (10,16,23,32), and molecular data are available only for chlorite dismutase (2, 11). The first step in microbial perchlorate reduction is the reduction of perchlorate (ClO 4 Ϫ ) to chlorite (ClO 2 Ϫ ) by the perchlorate reductase enzyme. To date, data are available for purified perchlorate reductase from two perchlorate-reducing bacteria, strains GR-1 and perc1ace (16, 23). The GR-1 analysis revealed an oxygen-sensitive periplasmic enzyme that resembled known nitrate and selenate reductases in both subunit and metal co...