The Natura 2000 ecological network is the largest network of protected areas in the world. The legal framework for its conservation is contained in the Birds Directive and the Habitats Directive, which are implemented by all EU Member States. Natura 2000 sites are divided into Areas of Importance for Birds (POP) and Areas of Importance for Species and Habitat Types (POVS). This paper provides an insight and overview of Natura 2000 sites in the County of Istria based on the analysis of data from the Bioportal. All target species within the target habitats are presented and threats and pressures are systematized. In addition, data from Natura 2000 sites in Istria were compared with the areas of the Ecological Network on the Pelješac Peninsula in order to compare their Natura 2000 sites (POVS and POP). Data from the Bioportal were processed in Excel, where a comparison of the percentage of spatial representation of area types (POP and POVS) was made on the two largest Croatian peninsulas. Istria has a very rich biological diversity with more pronounced pressures and threats, compared to Peljesac.