Long-term preservation of habitats has become a cornerstone of modern conservation policies. As resources allocated to conservation actions are often limited, developing relevant prioritizing methods is necessary. Although many studies have been published on species prioritization, habitats have been the subject of less research. This study aims to develop a simple prioritization method suitable for habitats and appropriate to any typology. We analyzed literature to select criteria that would be the most accurate to rank habitats. Our final method consists in calculating a score based on four criteria: legal obligation, territorial responsibility, conservation condition and an extra criterion designed to fit local interests and objectives. The method is applied on habitats listed in Annex I of the Habitats Directive (92/43/EEC) on the territory of RESEDA-Flore, a network of stakeholders involved in the conservation of Mediterranean flora. Results highlight that dune habitats show the highest conservation values, while rocky habitats and caves obtain relatively low scores. At the top of the ranking, Mediterranean temporary ponds (3170), Dunes with Pinus pinea and/or Pinus pinaster forests (2270) and Coastal dunes with Juniperus spp. (2250) appear to be a high priority. These results can be used to design and implement habitat conservation strategies in the French Mediterranean.