Abstract—Azoreductase is an FMN-dependent and NADH dependent enzyme of Escherichia coli. This enzyme is responsible for the degradation of azo dyes. In this study, we retrieved the crystal structure of the enzyme from PDB and 18 azo dyes from NCBI PubChem compound. These azo dyes were then docked with the FMN- dependent NADH-azoreductase enzyme to analyze the binding affinity of the azo dyes with the enzyme and predict the catalytic sites. In this approach, we identify the catalytic residues of FMN-dependent and NADH dependent enzyme of Escherichia coli which were then evaluated in terms of properties including function, conservation, hydrogen bonding, B-factor and flexibility. The results indicate that Phe-172, Glu-174, Lys-145, Asp-146 and Lys-169 play an important role as catalytic site residues in the enzyme. It is hoped that this information will provide a better understanding of enzyme mechanisms and also used to improve the designing strategies for dyes detoxification. In this study, the approach emphasises on a better understanding of the biodegradation of some of the commercially important azodyes mediated by azoreductase from E. coli. Furthermore, the catalytic site residues information is essential for understanding and altering the substrate specificity and for the design of a harmless azodye.