Recently, there has been an augmenting demand for chitosan-metal nanocomposites in biomedicine as drug delivery and diagnostic agent due to their notable e cacy and desired biocompatibility. In this present study, chitosan-selenium nanocomposite (CS-SeNC) prepared by in vitro, economical green chemistry principle was evaluated for quorum quenching activity against quorum sensing virulence genes expression in the human pathogenic multidrug-resistant bacterial pathogen Pseudomonas aeruginosa. Biocompatibility of the synthesised CS-SeNC was evaluated on the zebra sh model by determination of expression pattern of oxidative stress enzymes genes -catalase (CAT), superoxide dismutase (SOD1), apoptosis genes p53 and Bax genes in liver tissue. Histopathological analysis of the liver was also conducted. The silencing effect of the synthesised nanocomposite on major virulence factors encoding genes Las B and RhII was investigated by determining relative gene expression rate adopting quantitative real-time reverse transcriptase-polymerase chain reaction. This is followed by studies that measure relative gene expression of respective quorum sensing genes, the effect of CS-SeNC on the quorum sensing genes mediated virulence factors like bio lm formation, pyocyanin production, swarming motility and elastase activity were demonstrated. Relative gene expression of both the genes was signi cantly reduced in all the dosages of CS-SeNC treatment, with subsequent reduction in the production of all the tested virulence factors of P.aeruginosa. The absence of marked expression of oxidative stress enzymes genes apoptosis genes in the CS-SeNC administrated zebra sh model reveals the best biocompatibility. Liver histology has not shown any marked effect, con rming the best biocompatibility. The present study implies that CS-SeNC prepared by in situ green science principles is the promising antibacterial agent against multiple drug-resistant bacterial strains, which exhibit an antagonistic effect by inhibiting the molecular mechanism of pathogenesis with noteworthy biocompatibility.