The research carried out in the three foundational sites of the Chilean Long-Term Socio-Ecological Research Network (LTSER-Chile) aims to answer questions that reflect the regional context in which each site is immersed. The formation of the network in 2008 provided an opportunity to establish comparative studies and analyse the effects of the different components of global change could exert on different ecosystems in Chile. This study presents an analysis of the research programs of each of the three sites and presents the context in which these lines have been established. Each founder site has identified key aspects associated with local needs and the interests of the research groups that initiated and have directed the ecological or socio-ecological long-term studies. At the national scale these different approaches are complementary. First, we present an analysis and evaluation of the research conducted by each of these groups. Then, we develop a diagnosis of the research developed at each of the sites during the last two decades with the goal of identifying gaps and future research opportunities. Furthermore, this characterization will contribute to addressing the challenges and opportunities in basic and applied long-term socio-ecological research.