Problem statement: Ethanol production from sugarcane molasses generate large volume of effluent containing high Biological Oxygen Demand (BOD) and Chemical Oxygen Demand (COD) along with melanoidin, a color compound generally produced by "Millard reaction". Melanodin is a recalcitrant compound degraded by specific microorganisms having ability to produce mono and dioxygenases peroxidases, phenoxidases and laccases, are mainly responsible for degradation of complex aromatic hydrocarbons like color compound. These compounds causes several toxic effects on living system, therefore may be treated before disposal. Approach: The purpose of this study was to isolate a potential thermotolerant melanoidin decolorizing bacterium from natural resources for treatment of distillery effluent at industrial level. Results: Total 10 isolates were screened on solid medium containing molasses pigments. Three potential melanoidin decolorizing thermotolerant bacterial isolates identified as Bacillus subtilis, Bacillus cereus and Pseudomonas sp. were further optimized for decolorization at different physico-chemical and nutritional level. Out of these three, Bacillus subtilis showed maximum decolorization (85%) at 45°C using (w/v) 0.1%, glucose; 0.1%, peptone; 0.05%, MgSO 4 ; 0.01%, KH 2 PO 4 ; pH-6.0 within 24h of incubation under static condition. Conclusion/Recommendations: The strain of Bacillus subtilis can tolerate higher temperature and required very less carbon (0.1%, w/v) and nitrogen sources (0.1%, w/v) in submerged fermentation. It can be utilized for melanoidin decolorization of distillery effluent at industrial scale.