This study aims at investigation of antibacterial property of Parthenium hysterophorous against aquatic bacterial pathogens and to identify the key bioactive compound of the same. Antibacterial activity of the crude extracts confirmed that chloroform extract PHC has strong antibacterial activity against aquatic pathogens V.anguillarum and V.harveyi with 16mm and 15mm ZOI at 1mg/well concentration. The crude extracts were subjected for GC-MS analysis to identify the secondary metabolites. PHC was subjected to silica-gel column chromatography to separate the individual phytochemicals. PHC was separated into 9 fractions, among which Fraction No.2 demonstrated significant antibacterial activity against V.anguillarum and V.harveyi with 19mm and 17mm ZOI at 10µg/well concentration. Fraction No.2 was identified to be β-sitosterol based on mass spectrometry analysis and fragmentation analysis. In-silico protein ligand docking demonstrated that β-sitosterol has highest affinity to inhibit dihydrofolate reductase (DHFR) enzyme with -10.10Kcal/mol binding energy. This prediction was further validated using molecular dynamic simulation for 20ns. Based on these computational analyses, it was proposed that β-sitosterol exhibits antibacterial activity via inhibition of DHFR enzyme. β-sitosterol is a well known nutritionally valuable compound that reduces cholesterol levels in humans. It is also been used as supplement feed to increase the nutritional value of cultured fishes. β-sitosterol has also been proven to have positive effect in growth and reproduction of cultivated fishes. Findings of this study strongly suggest the usage of β-sitosterol in aquaculture, as nutritional supplement and also as disease control agent to prevent and control fish diseases caused by Vibrio species.