This paper argues that due to the co-evolution of biological and cultural diversity, a meaningful study of biodiversity must be positioned within complex social-ecological systems. A complex systems framework is proposed for conceptualising the study of social-ecological systems. A case study approach is adopted whereby changes in biodiversity on the Causse Mejan, France, are linked with changes in society, land use, agricultural practices and policies. We argue that ecological and social resilience is linked through the dependence on ecosystems of communities, and in turn by the influence of institutional structures, including market forces, on the use of natural resources. Within a non-equilibrium evolutionary perspective, we highlight the difficulty of choosing a landscape and biodiversity of reference and postulating that it is in equilibrium with a type of social organisation. We conclude by exploring an 'adaptive management' approach to the management of the biodiverse landscape studied.