One of the core European Union environmental policies is the creation and monitoring of the Natura 2000 network of protected areas. This network has been explicitly established for the preservation of conservation priority habitat types and species. Still the concept of habitat is a key concept for ecologists that remains ill defined and is notoriously hard to quantify and measure. Several classification schemes have been put forward, but their relative strengths and weaknesses remain less well examined. In this study we analyzed 8 different Natura 2000 sites (3 Greek, 2 Italian, 2 Portuguese, 1 British). Our study sites reflect a variety of ecosystems, most of them are Mediterranean (7 of the 8) and most of them are wetlands (6 of the 8). In each site, we classified habitats according to 4 different classification schemes (Annex I of the Habitats Directive, Corine Biotopes, EUNIS and General Habitat categories). Also, we used three other widely used land cover classification schemes (namely Corine Land Cover, FAO Land Cover Classification System and IGBP DIS scheme). We found that the different schemes produced considerably different values of landscape diversity leading even to different ranking of the sites according to their diversity. Furthermore, when comparing the landscape composition among sites according to the different schemes, they led to different inferences. Our results imply that the classification scheme used for estimating habitat composition plays an important role for the monitoring of protected areas, perhaps more important than previously assumed.