The review reveals secondary metabolites (terpenes, alkaloids, flavanoids,phenols etc) which shows a wide range of pharmacological activities like antihypertensive effects, antimalarial activity, anticancer actions, antioxidants, anti-inflammatory, antidiarrhoeal, cytotoxic, antiparasitic, antibacterial, antifungal and antiviral activities.The study will help the researcher for identification of individual gene families for making secondary metabolites from different plants and makes it possible to conduct comparative genomic analysis. This review indicates the significance for the research in developing the plant gene target methods which will help for the extensive growth and development of medicinal plant. However, with the help of new methodology and analytical techniques many more of these phytochemicals can be identified and the development of more isolation can be done. Secondary metabolite plays an important role of many bioactivities. Based on many published paper, indigenous medicinal plants of India would emerge to be a hopeful source of novel drugs can be used as potentially of new pharmaceuticals. There is a urgent need for advance research and further investigations of endemic plants and their constituents are required to entirely know the molecular mechanisms of their action in vitro and in vivo with the aids to guarantee the plant extracts are safe for human can be use in market as proof based medicines.