This study deals with the characterization of rhizosphere bacterial communities and metabolic products produced during the two stage sequential treatment of post methanated distillery effluent by bacteria and constructed wetland plants. Results showed that bacterial treatment followed by wetland plants (Phragmites cummunis) resulted 94.5% and 96.0% reduction in BUD and COD values, respectively. The PCR-RFLP analysis showed the presence of Stenotrophomonas, Enterobacter, Pantoea, Acinetobacter and Klebsiella sp., as dominant rhizosphere bacterial communities which play an important role in degradation and decolorization of PMDE in wetland treatment system. Further, the LC-MS-MS and other spectrophotometric analysis have shown that most of the pollutants detected in untreated PMDE were diminished from bacteria and wetland plant treated PMDE indicating that bacteria and wetland plant rhizosphere microbes utilized them as carbon, nitrogen and energy source. While, methylbenzene, furfuryl alcohol, and 4-vinyl-2-methoxyphenol were detected as metabolites in bacteria and hexadecanol in wetland plant rhizosphere treated PMDE. (C) 2011 Elsevier Ltd. All rights reserved.