Human dependence on forests can have manifold ecological consequences from the level of genes to the entire ecosystem. Despite the extensive use of forest products by communities, especially in tropical countries such as India, there have been hardly any attempts at monitoring these consequences. Understanding the consequences could facilitate the development of management protocols that, while maintaining the livelihoods of the forest-dependent communities, could help minimise the associated ecological cost. In a unique attempt over the last decade, we have examined the ecological consequences of forest use, from genes to ecosystem, in the Biligiri Rangaswamy Temple Wildlife Sanctuary, south India. In this article we review these findings and demonstrate that monitoring of biodiversity elements from genes to ecosystem is important in understanding the underlying process of change and in formulating appropriate strategies for the conservation of biodiversity.