Azo dyes are widely used in the textile industry despite being poorly biodegradable and highly toxic. Hence, azo dyes need to be removed from effluent prior to environmental discharge. Microbial communities are efficient for the degradation and mineralization of azo dyes. However, little is known about the functional microbial communities responsible for the degradation process. In this study, a novel indigenous bacteria consortium was developed for characterizing the functional microbial communities involved in the degradation of a sulfonated azo dye, Direct Blue 2B (DB2) in a simple batch reactor. The optimal temperature, pH, and salinity for the decolorization process were 38.70 °C, pH 7.57, and 20.10 g L−1 NaCl, respectively. The effect of the operating conditions on microbial community structure were determined using high-throughput Illumina HiSeq sequencing. Gammaproteobacteria, Betaproteobacteria, and Bacilli were dominant under most of the operating conditions. At pH above 8 and NaCl concentration above 30 g L−1, Firmicutes relative abundance did not significantly change suggesting tolerance towards alkaline and hypersaline environments. Tritium aestivum and Glycine max seed germination following exposure to YHK treated DB2 solution was above 80% compared to 50% in untreated DB2 solution. The YHK consortium decolorized dyes structurally different from DB2 such as trimethyl phenyl and direct dyes. The results of this study offer valuable data on improving optimization of dye biodegradation processes and the capability of YHK in in situ bioremediation.