The present study reveals the benzene degrading potential of bacterial species isolated from petroleum contaminated soil. Genomic analysis suggests that Bacillus sp. M4 was found to be dominating species. The process parameters were optimized and found to be pH 7.0 +/- 0.2, temperature 32 +/- 5 degrees C, immobilization time (20 days) and benzene concentration 400 mg/L. The maximum removal efficiency of benzene was calculated and found to be 93.13% at elimination capacity 156 (mg/L/day) and inlet loading rate 192 (mg/L/day) achieved in 54th days of operation. In the study, the residual metabolites were analyzed by GC/MS analysis and identified as benzene-1, 2-diol. In order to identify the responsible protein involved in the process of benzene biodegradation The proteomic study was performed and proteins were identified by MALDI-TOF analysis. The molecular docking was confirmed by the benzene biodegradation.