Perchlorate is an emerging surface water and groundwater contaminant, and it is of concern because of its mobility in the environment and its inhibitory effect on thyroid function. Microbial fuel cells (MFCs) may be a suitable method for its treatment. We investigated a MFC with a denitrifying biocathode for perchlorate reduction and utilized the system to identify putative biocathode-utilizing perchlorate-reducing bacteria (PCRB). Perchlorate reduction in the MFC was established by increasing the perchlorate loading to the biocathode, while decreasing nitrate loading. Perchlorate reduction was obtained without the need for exogenous electron shuttles or fixed electrode potentials, achieving a maximum perchlorate removal of 24 mg/L-d and cathodic conversion efficiency of 84%. The perchlorate-reducing biocathode bacterial community, which contained putative denitrifying Betaproteobacteria, shared little overlap with a purely denitrifying biocathode community, and was composed primarily of putative iron-oxidizing genera. Despite differences in cathodic function, the anode communities from the perchlorate-reducing MFC and the denitrifying MFC were similar to each other but different than their corresponding biocathode community. These data indicate that PCRB can utilize a cathode as an electron donor, and that this process can be harnessed to treat perchlorate while producing usable electrical power.