Fruits of Pedalium murex known as, ‘Gokhru’ is predominantly used in Ayurveda for its aphrodisiac properties and use in treatment of urological orders. However till now, bioactivity of this fruit has not been documented for plant protection against phytopathogenes, Hence in this regard, we investigated antimicrobial activity of P. murex fruit extracts (isolated from the different agro climatic zones of India) were tested against twelve microbial phytopathogens. From 29 fruit extracts, only 13 were found to be active against three pathogens viz. Botrytis cinerea, Rhizoctonia solani, and Sclerotinia sclerotiorum. Among the nine TLC fractions only one showed presence of a single peak, thus presence of a single compound in the crude extract. Based on lower IC₅₀ value (328 μg/ml) the crude fruit extract collected from Indore region was further characterized. Evaluation against screened phytopathogens indicates its activity. Further, structural characterization of this compound using FTIR and NMR revealed it to be a novel compound i.e. 5-β-Hydroxyl tridecanyl benzoate. Our study paves a way to investigate effective dose of P. murex fruit extracts to utilize in plant protection programs. In future, a better method is required to scale up the process of bioactive molecule (5-β-Hydroxyl tridecayl benzoate) extraction from P. murex or for its chemical synthesis.