Nutrient rich niche provided by plants supports the growth of various microbes, some of which form mutualistic association and colonize healthy plant tissue intercellularly and/ or intracellularly forming asymptomatic as-sociation and constitute important components of plant micro-ecosystem. Endophytes maintain a stable sym-biotic association with plants and the long period of co-existence and evolutionary processes have led to evolution of biosynthetic capability to synthesize a wide range of metabolites. Biosynthetic potential of endo-phytes from medicinal plants represent an attractive source for discovery of metabolites for application in pharmaceutical, agricultural, food and cosmetic industries. Various studies have reported hundreds of natural products including alkaloids, terpenoids, flavonoids and steroids from endophytes. Many of these bioactive endophytes exhibit antimicrobial, antioxidant, immunosuppressive and cytotoxic properties besides their puta-tive use as biocontrol agents. Present review documents the various pharmaceutically relevant metabolite(s) identified from endophytes isolated from plants growing in different ecological niches. The review also discusses the studies undertaken towards epigenetic modifications of biosynthetic gene clusters of endophytes for acti-vation of silent or cryptic genes.