Detoxification of perchlorate by microbial communities under denitrifying conditions has been recently reported, although the identity of the mixed populations involved in perchlorate reduction is not well understood. In order to address this, the bacterial diversity of membrane biofilm reactors (MBfR) set up under autotrophic denitrifying and perchlorate-reducing conditions were examined by analyses of the 16S rRNA gene sequences of clone libraries. Inocula from diverse locations were tested for their ability to reduce nitrate and perchlorate in synthetic ion exchange spent brine (45 g/l NaCl) using H(2)-based MBfRs. Phylogenetic analysis of 16S rRNA gene sequences showed that proteobacterial species dominated the biofilm communities, particularly nitrate-reducing gamma-proteobacteria. Even though the inocula to the MBfRs came from different sources, clones closely related to Marinobacter hydrocarbonoclasticus represented 53% of all clones in the MBfR biofilms. The clone libraries contained no known perchlorate-reducing bacteria, which suggest that denitrifiers carried out perchlorate reduction, probably by secondary-utilization. Published by Elsevier Ltd.