A potential bacterium Bacillus flexus RMWW II has been isolated from rice mill effluent, and examined for its decolorizing potential for lignin-mimicking dyes. The biodegradation of alkali lignin by the rod-shaped, Gram-positive, oxidase and catalase-positive Bacillus flexus RMWW II bacteria is due to its uptake of lignin as the sole carbon source. The lignin degradation was 100% at a lignin concentration of 50 mg L−1 but the degradation reduced to 20% at 400 mg L−1. The bacterial-mediated biodegradation of alkali lignin was suitably explained by the Edward kinetics model with a maximal specific biodegradation rate (qmax) of 0.056 h−1 and true specific biodegradation rate (q*) of 0.042 h−1. The non-toxic nature of the metabolites of alkali lignin after bacterial degradation was illustrated by phytotoxicity studies. This bacterium was utilized to treat complex rice mill wastewater, as lignin is one of the major components of the effluent. A considerable reduction of 84% of chemical oxygen demand (COD) was observed in a batch reactor in 70 h of operation. The bacterial treatment results for the actual rice mill effluent indicate that Bacillus flexus RMWW II could be a promising agent for microbial remediation of lignin-laden raw rice mill wastewater.