The innate immune system in primitive organism of earthworms belonging to the invertebrate Phylum of Annelida, exhibits advanced functional features and plays role in conferring immunity. The innate immune system of earthworms, consist of phenoloxidase system (POS), pattern recognition rectors (PRRs), Toll like receptors (TLRs), antimicrobial peptides (AMPs) coelom cytolytic factor and lysenin that confer immunity to the soil dwelling earthworms and is continuously exposed to pathogens and pollutants, however detailed mechanism of their function remains largely unknown. In this article we have (i) studied the wild type lysenin from Eisenia fetida (E fetida) (ii) identified the binding pocket and (iii) studied the binding of wild-type lysenin from E fetida with membrane protein of Shigella flexneri (S flexneri) by insilico methods of protein-protein docking. We have tried to understand the implications of lysenin in targeting pathogen by using the Cluspro 2.0 and Schrodinger protein-protein docking tool. This is the first report of structure and functional insilico based study of lysenin binding to bacterial surface protein, providing an insight of the mode of action of lysenin in conferring immunity against S flexneri infection with a potential application as an antibacterial agent.