Purified glycosides, Isoquercetin and Cassinopin from Crotalaria candicans were selected for the synthesis of biogenic copper nanoparticles (CuNPs).The designed biogenic CuNPs was characterized and when evaluated against panel of gram negative and positive bacteria, the biogenic CuNPs were found to be more effective against methicillin resistant Staphylococcus aureus (MRSA). Antibacterial, anti-biofilm effects and time kill studies confirmed the ability of biogenic CuNPs to curtail MRSA. Scanning electron microscopy, Crystal violet staining and fluorescent live-dead imaging showed that treatment with sub lethal levels of glycoside capped CuNPs resulted in greater than 50% decline in biofilm formation by MRSA, which implies that anti-biofilm effect of biogenic CuNPs is not dependent on antibacterial effect. Alizarin red assay implied that prolonged treatment of biogenic CuNPs in presence of MRSA, releases Cu(II) ions and hence antibiofilm effect is primarily mediated by NP and is not due to released Cu(II) ion. The NPs caused altered membrane permeability and reduced surface hydrophobicity, thus accounting for its antibiofilm effect.