Plant molecular farming has made an extensive development and is an attractive and widely accepted powerful technology for extraction of pharmaceutical products from plants. The present research work focuses on the study of root exudates induced in the host plant by root colonizing endophytes. The fungus            Piriformospora indica imparts growth promotion and uptake of various nutrients by host plant. The fungus also mediates production of bioactive components during colonization and the active compounds are released out by host plants through root exudates, which is evidenced during hydroponic cultivation. The root exudates from hydroponic study were subject to GC-MS assay.  The P. indica colonization in Setariam italica  (L.) P. Beauvois plant has been observed and exudated compounds were found to include bioactive compounds identified through GC-MS analysis peaks showed production of compounds viz.,m-Hydroxyphenylacetic acid , Oxime-methoxy phenyl, 4-Ethylbenzoic, Cyclopentylester, 4-Nitrocinnamaldehyde, Benzaldehyde;4(1,3-dioxolanzyl). Endophyte colonized plants secreted compounds related to various biological activities; increase in hormone production, antipathogenic activity, metabolic activity, increase the uptake of nutrients, and antioxidant property. The endophyte may be used for production of plant bioactive compounds through hydroponics and root exudate extraction.