Perchlorate bioreduction coupled to methane oxidation was successfully achieved without the addition of nitrate or nitrite in a membrane biofilm reactor (MBfR) inoculated with a mixture of freshwater sediments and anaerobic digester sludge as well as return activated sludge. The reactor was operated at different methane pressures (60, 40 and 20 Kpa) and influent perchlorate concentrations (1, 5 and 10 mg/L) to evaluate the biochemical process of perchlorate bioreduction coupled to methane oxidation. Perchlorate was completely reduced with a higher removal flux of 92.75 mg/m(2).d using methane as the sole carbon source and electron donor, other than hydrogen or other limiting organics. Quantitative real-time PCR showed that bacteria prevailed over archaea and the abundances of mcrA, pMMO, perA, and nirS genes were correlated with the influent perchlorate flux. High-throughput sequencing of 16S rRNA genes demonstrated that the functional community consisted of methanotrophs, methylotrophs, perchlorate-reducing bacteria, as well as various denitrifiers.