The world‘s biodiversity is currently in rapid decline - Europe being no exception - with as principal cause a human-mediated global change. The Natura 2000 network is an important conservation tool for European biodiversity; it is a network of natural and semi-natural sites within Europe with high heritage values due to the exceptional flora and fauna they contain. Here, we evaluated the coverage of 300 threatened species by the Natura 2000 network, and determined potential factors influencing the designation of sites and the structure of the network within a country (social, ecological and demographic national factors). Our analysis was based on a coverage ratio between the Natura 2000 sites and distribution maps of threatened European species. We showed that the distributions of a large proportion of threatened species of mammals, birds and reptiles considered in our study were highly covered (above 90%) by the current Natura 2000 network, demonstrating that the Natura 2000 network also covers species not listed in the annexes of the Nature Directives. However, our results confirm that a large proportion of threatened species (some of them listed on the European annexes), especially fishes, are currently poorly covered by the Natura 2000 network. The coverage of species likely seemed to be highly related to national demographic factors, i.e. the proportion of the national urban population. Our analysis also suggested that the designation of sites depends too strongly on governmental politics, economic and cultural criteria, and interactions between society and the environment. A more effective process might be necessary to ensure the Natura 2000 network reaches its potential as the most important and comprehensive network of protected areas intended to halt the loss of biodiversity in Europe in the near future.