The Mediterranean basin, is subject to deep demographic changes, a high rate of urbanization with about three quarters of its population in cities 2030, a fast economic growth on the Eastern and Southern shores over the last 15 years, submitting biodiversity and ecosystems of this “hotspot” area to massive anthropogenic pressures. Challenges for research are multiple: identifying, categorizing, and deepening knowledge of the exposed ecosystems of the basin, in relationship with the services they supply and with biodiversity, assessing their short term and long term risks, and discussing their values from the different standpoints proposed in the literature, studying and designing methods for valuing and managing them when their functioning is dynamically interrelated with the social and economic activities. This program integrates researchers from the social and the natural sciences and therefore requires defining and clarifying in common the key concepts and theoretical frameworks used: dynamics of biodiversity in relationships with anthropogenic activity, ecosystems services, risks and vulnerability, values and valuation of ecosystems over different horizons of time, management of ecosystems and the institutions where it takes place, social attitudes and representations of biodiversity, conservation policies. Beyond biodiversity and the diversity of its climates and landscapes, the Mediterranean basin is also a “hotspot” of nations, cultures, political systems, migrations, and economic exchanges. So, knowledge of the biodiversity dynamics and the ecosystem services in the basin should rely greatly on case studies reflecting this diversity.