The Natura 2000 framework is the centrepiece of EU nature and biodiversity policy. The foundations of this framework are two European directives: the Birds Directive and the Habitats Directive. It is reported in scientific literature that member states encounter problems when implementing the framework. In this research project, we studied and compared problems encountered by Greece and Spain on the implementation of Natura 2000, using three different methodologies. We used an intensive literature review, a survey conducted among Greek and Spanish academics involved with Natura 2000 and a bibliometric study. The combined results of these different methods allowed us to illustrate and, where possible, explain the problems encountered with the implementation. Some problems were encountered by more member states and could be considered inherent to the framework, others were shown to be related specifically to the Mediterranean area and some were country specific. We found causes for these problems linked to differences ecology, economy and culture.