Dye degradation has gained attention of late due to indiscriminate disposal from user industries. Enhancing efficiency of biological treatment provides a cheaper alternative vis-a-vis other advanced technologies. Dye molecules are metabolized biologically via anoxic and oxic treatments. In this study, bacterial community surviving on dye effluent working in anoxic-oxic bioreactor was analyzed using 16S rDNA approach. Azo-dye decolorizing and degrading bacterial community was enriched in lab-scale two-stage anoxic-oxic bioreactor. 16S rDNA metagenomic libraries of enriched population were constructed, screened and phylogenetically analyzed separately. Removal of similar to 35% COD with complete decolorization was observed in anoxic bioreactor. Process was carried out by uncultured gamma proteobacterium constituting 48% of the total population and 12% clones having homology to Klebsiella. Aromatic amines generated during partial treatment under anoxic bioreactor were treated by aerobic population having 72% unculturable unidentified bacterium and rest of the population consisting of Thauera sp., Pseudoxanthomonas sp., Desulfomicrobium sp.. Ottowia sp., Acidovorax sp., and Bacterioderes bacterium sp. (c) 2009 Elsevier Ltd. All rights reserved.