Molecular docking is routinely used for understanding drug-receptor interaction in modern drug design. Here we described the docking of benzimidazole containing isoxazole derivatives as inhibitors to Escherichia coli. The inhibitory activities against Escherichia coli β-ketoacyl-acyl carrier protein synthase III (ecKAS III) were investigated by molecular docking using the HEX docking software. All the designed compounds were showed good binding energy when compared with the binging energies of standard drugs such as Ciprofloxacin (-211.04), Amoxilin (-182.23) and cefotaxime (-207.62). Among all the designed compounds, the compound 3 shows more binding energy values (-298.32). Further we planned to synthesis these benzimidazole derivatives and screen for in-vitro anti bacterial effect on Escherichia coli and other micro organisms.