Phytophthora meadii is a fungal species which causes Fruit Rot Disease (FRD) in Areca catechu affects the quality and yield which is main threat for agricultural economy. Traditional methods include chemical fungicides like bordeaux mixture, Fosetyl-al, metalaxyl, mancozeb, copper oxychloride, cymoxalin, copper sulfate, etc in treatment of FRD, which can lead to environmental and health issues. In this study, an in silico approach was employed to identify potential bioactive compounds that could serve as effective agents against the pathogens responsible for FRD in Areca catechu. Utilizing a combination of molecular docking and virtual screening, we screened a comprehensive library of natural compounds for their ability to inhibit key enzymes and proteins associated with FRD pathogens. The molecular docking analysis focused on identifying compounds with high binding affinities to target proteins, suggesting their potential efficacy in disrupting pathogen activity. Among the screened compounds, several compounds have shown strong binding affinities indicating their potential as bioactive agents against FRD pathogens. These findings provide a promising foundation for the development of natural, environmentally-friendly treatments for FRD in Areca catechu.