Perchlorate, an oxyanion of chlorine is now recognized as a widespread ion in environmental systems. Because of the potential health complications associated with prolonged exposure, perchlorate was added to the EPA's Contaminant Candidate List in 1998. Subsequent remediation efforts have led to the recognition of microbial reduction as the preferential strategy to remove perchlorate. Dissimilatory perchlorate-reducing bacteria (DPRB) can use perchlorate as a terminal electron acceptor, respiring it to harmless chloride, and are ubiquitous in the environment. The perchlorate/chloride couple is highly favorable thermodynamically, however, many DPRB only make use of perchlorate after complete reduction of nitrate, a less thermodynamically favorable electron acceptor. Given that perchlorate and nitrate are common co-contaminants, understanding the mechanism of this regulation is important for optimization of bioremediation strategies in mixed-waste treatment schemes. The recent completion of the whole-genome sequence of the perchlorate-reducer, Dechloromonas aromatica RCB, has offered further insight into the evolution and regulation of this unique metabolism. Genomic and transcriptomic analysis has yielded considerable understanding of the mechanism by which this environmentally important organism regulates its responses to alternative electron acceptors, including nitrate and perchlorate.