Biodiversity is declining worldwide under increasing human pressure. Since the location of and the threats are unevenly distributed and the resources available for conservation are limited, prioritization is essential to reduce the losses. Most conservation efforts until now proved to be ineffective in stopping the present worldwide decline of threatened species. We focus on the European Union (EU) after the repeated enlargements in the last decade, from 15 to 27 countries, by considering the present conservation priorities that have shifted towards a continental scale approach. The situation in the EU indicates that despite the differences in wealth across countries, there are no significant differences in the number and surface of protected areas between them, so re-evaluating conservation priorities at a continental scale and a reallocation of funds is required. A major limitation in priority settings for conservation is data availability. We recommend including in the decision process data provided by phylogeographic studies. This will prevent the decline of populations and species with evolutionary potential from centres of speciation and climate refugia. Recent EU members from central and eastern Europe still retain high biodiversity with a rather good conservation status. A large number of areas with high evolutionary potential identified by phylogeographic studies are located there and should be considered priorities within the context of global changes, as a proactive approach. We recommend a periodic re-evaluation of the status of species and habitats based on current research results, harmonization between the priority species listed in the conventions, directives and Red Lists at both EU and national levels.