Five aerobic enrichments efficient at degrading methyl tert-butyl ether (MTBE) under different substrate conditions were developed in well-mixed reactors containing a polyethlene porous pot for biomass retention. The five substrate conditions were as follows: MTBE alone; MTBE and diethyl ether (DEE); MTBE and diisopropyl ether (DIPE); MTBE and ethanol (EtOH); and MTBE with benzene, toluene, ethylbenzene, and xylene (BTEX). All five cultures demonstrated greater than 99.9% removal of MTBE. Addition of alternative substrate was found to have no effect on the performance of the reactors. The bacterial communities of the reactors were monitored periodically by denaturing gradient gel electrophoresis (DGGE) to determine when homeostasis was achieved. Phylogenetic analysis of the excised DGGE bands was done in order to compare the bacterial community compositions of the reactors. All cultures were found to be mixed cultures, and each enrichment was shown to have a unique composition. A majority of the bands in all reactors represented a group of organisms belonging to the Cytophaga-Flexibacter-Bacterioides (C-F-B) Phylum of bacteria. This was also the only group found in all of the reactors. This study demonstrates that MTBE can be degraded effectively in bioreactors under several substrate conditions and gives insight into the microorganisms potentially involved in the process.