The Mediterranean Sea is a hot spot of biodiversity. Current protection measures are stili poorly designed. The Aichi target requires the inclusion of at least 10% of the sea surface under some form of protection by 2020, while currently the MPA encompass approximately the 4% of the Mediterranean Sea, and this percentage drops to 0.4% if the Pelagos Sanctuary is not taken into account. Here, spatial priorities for the conservation of key Mediterranean habitats were identified through a systematic planning approach using a collection of georeferenced fine scale data of priority habitats (Posidonia meadows, coralligenous outcrops) and essential fish habitats (i.e. nurseries, spawning grounds) analyzed with the software Marxan. Our best protection scenario based on habitat distributions data covers the 13% of the basin and expands present conservation plans to areas that are generally neglected ( deep-sea, eastern basin). The percentage of overlap between the current conservation measures and the Marxan scenario produced in this study are about the 50% of the priority areas identified.