1. The relentless increase in both human activities and exploitation of marine resources is a threat to marine habitats and species. 2. For marine systems, several protection initiatives have been outlined over the past decade to significantly reduce the current rate of biodiversity loss at global, regional, and national levels, and to establish representative networks of marine protected areas with the aim of protecting 10-30% of marine habitats. 3. Reliable estimates of the total area occupied by each habitat are crucial to set adequate protection initiatives. Habitat mapping requires a sound habitat classification. Many classification schemes have been developed in different areas of the world, sometimes based on questionable criteria. 4. A critical analysis of the most recent marine habitat classification list produced for the Mediterranean Sea from the Regional Activity Centre for Specially Protected Areas (RAC/SPA) showed that (i) 39% of habitats and associated species considered in the list are scarcely covered by scientific knowledge from Web-based resources; (ii) 62% of the species/genera included in the list are primary producers; (iii) quantitative information about the geographical distribution of selected habitats and associated species is scant; and (iv) when available, information is largely unbalanced and biased towards the shallow western Mediterranean Sea. 5. Improved inventories of marine habitats are needed to support accurate and consistent mapping activities. The combination of large-scale mapping and sound habitat classifications will allow better estimates of biodiversity distribution, to reverse regional/global habitat loss rates through the achievement of conservation targets and deadlines that, for the moment, are systematically not met.