This paper clarifies the provisions of EU legislation concerning the nature protection which have established the ecological network Natura 2000 (Directive 2009/147/EC on the conservation of wild birds and Directive 92/43/EEC on the conservation of natural habitats and of wild fauna and flora). For this purpose, the paper presents the judgments of the Court of Justice of the European Union concerning the interpretation of the provisions of the respective directives. The goal is to provide with an answer to the question regarding the process of establishment of the ecological network Natura 2000 and the level of nature protection which Member States must provide when they are approving projects that may have adverse impacts on the protected areas. The paper then analyses the process of establishing the Natura 2000 network in Croatia. Since the process of establishing the ecological network can last for years, special attention is paid to the question of the moment from which the Member States are obliged to protect the areas that will become Sites of Community Importance when they are adopted by the European Commission. The paper also points to the problem of non-compliance of certain basic terms in the translation of the EU legislation into Croatian. The paper, thus, clarifies certain differences in terminology that exist in the current Croatian legislation and its proposed amendments.