Abstract Geographical Information Systems (GIS) can be used in biological conservation as decision support systems, integrating the spatially referenced CORINE land cover and using data to assess whether natural protected areas cover particular types of ecosystems and/or biogeographical diversity. This study analyzes whether the Natura 2000 sites, which are Special Protection Areas and Special Areas of Conservation declared in Romania cover the diversity of wetlands and coastal areas habitats, as well as the biogeographical diversity. Results suggest that the situation is particularly good in the steppic and Black Sea regions, but could be improved in the continental, pannonian and alpine region. Increasing the surface of existing protected areas and declaration of new sites is already on the governmental agenda. The limitations of this methodology are related to the frequency of updating CORINE data at the scale of the entire continent.