The Iberian Peninsula is a major European region of biodiversity, as it harbours more than 30% of European endemic species. Despite a number of studies having evaluated the ability of nature reserves to protect certain taxa, there is still a lack of knowledge on how Iberian endemic fauna are represented in these reserves. Here, biodiversity hotspots of Iberian endemicity were detected and the effectiveness of the Natura 2000 network (N2000) in representing 249 endemic species from eight animal taxonomic groups (amphibians, mammals, freshwater fishes, reptiles, water beetles, butterflies, lacewings and dung beetles) was evaluated. Only 10% of these Iberian endemic species are considered species of community interest (i.e. species included in the Annexes of the Habitats Directive). Generally, N2000 is effective in its representation of Iberian endemic fauna, although species and few hotspots of endemism were still not represented. It is necessary to declare a few new protected areas, thus enhancing N2000's effectiveness in the conservation of the Iberian endemic fauna. Although the aim of N2000 is to protect species listed in the Birds and Habitats Directives, the conservation status of endemic species from one of the most important areas of Europe in terms of biodiversity, could be also a concern for the European Union. These results are useful in the context of the recent European Commission mandate calling for a ‘fitness check' of the Birds and Habitats Directives. This approach could be also applicable to other regions with high value of endemicity. informacion[at]ebd.csic.es Rosso et al (2017) Effectiveness of the Natura 2000 network in protecting Iberian endemic fauna. Anim Conserv Doi 10.1111/acv.12387