Use of the fuel oxygenate methyl tert-butyl ether (MTBE) has led to widespread environmental contamination. Anaerobic biodegradation of MTBE observed under different redox conditions is a potential means for remediation of contaminated aquifers; however, no responsible microorganisms have been identified as yet. We analyzed the bacterial communities in anaerobic-enriched cultures originating from three different contaminated sediments that have retained MTBE-degrading activity for over a decade. MTBE was transformed to tert-butyl alcohol and the methyl group used as a carbon and energy source. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes showed that the MTBE-utilizing microcosms established from different sediment sources had substantially different community profiles, suggesting that multiple species are capable of MTBE biodegradation. The 16S rRNA genes from one enrichment culture were cloned and sequenced. Phylogenetic analysis showed a diverse community, with phylotypes belonging to the Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Thermotogae. Continued enrichment on MTBE further reduced the community to three predominant phylotypes, as evidenced by T-RFLP analysis, which were most closely related to the Deltaproteobacteria, Firmicutes and Chloroflexi. These three common operational taxonomic units were detectable in the enrichments from Atlantic and Pacific coastal samples. Identification of the microorganisms important in mediating anaerobic MTBE transformation will provide the foundation for developing tools for site assessment and bioremediation monitoring.