Trichloroethylene (TCE), a common soil and groundwater pollutant, can be biodegraded either in aerobic and anaerobic conditions. Tartakovsky et al. (2003) have shown recently that the TCE degradation performances were higher in the coupled aerobic/anaerobic bioreactor (CANOXIS) oxygenated with hydrogen peroxide (H2O2) at a sub-bactericidal concentration than in an upflow anaerobic sludge bioreactor (UASB). To understand the microbial ecology underlying the TCE degradation in those reactors, a molecular study of the microbial population dynamics and a phylogenetic characterization were conducted using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The two bacteria domains and the presence of functional genes for TCE degradation were investigated using appropriate primers.