Due to widely expanding threats to the forests, protected areas may offer the best approach and prospect to conserve the biological diversity. However, there have been few studies that have emphatically demonstrated the role of protected areas in conserving the genetic diversity of plant species. We examined the population structure and genetic diversity of two economically important bamboo species, Bambusa arundinacea and Dendrocalamus strictus, in the core, buffer and the peripheral regions of the Biligiri Ranganathaswamy Temple Wildlife Sanctuary (BRTWS) at central Western Ghats, India. Our results indicate that the proportion of human disturbance on both the bamboo species were significantly less in the core and buffer regions of the BRTWS as compared to periphery. In both the bamboo species, the core and buffer regions maintained a better population stand. The frequency distribution of the genetic similarity indices of the core populations were found to be more widely distributed as compared to the peripheral populations. Our results strongly indicate the relevance of protected areas in maintaining the population structure and the genetic diversity of economically important plants such as bamboos that are otherwise prone to heavy extraction pressures.