Is the connectivity of the Natura 2000 network better across internal or external administrative borders?

•We analysed spatial and functional connectivity of site network across borders.•In Germany, Italy and Spain spatial connectivity was better across internal borders.•In the same countries functional connectivity was better across international borders.•In Austria spatial connectivity across internal borders was worse than elsewhere.•We explain this by the lack of coordination of Natura 2000 at the national level. The lack of coherence of a network of protected areas across administrative borders may occur as different bodies are responsible for nature conservation on either side which may lead to a lack of unified approaches in site selection. In the European Union such a situation is possible not only across international borders but also across borders of provinces of those countries which have strong legislative internal powers. We obtained robust estimates of spatial connectedness and functional connectivity, the latter based on presence of the same species in Natura 2000 sites adjoining across internal borders, between federal states of Austria and Germany and autonomous provinces of Italy and Spain. Network connectedness across internal borders in Germany, Italy and Spain showed a similar logical pattern with means over 75% and most values were higher than connectedness measures of international borders. In Austria we found no clear pattern: connectedness measures both of internal and external borders varied greatly. Network connectivity across internal borders was typically poorer than connectedness and poorer than connectivity of international borders of the same countries: we provide a number of possible explanations for that. The poor connectedness of the Austrian Natura 2000 network across internal borders is linked with the absence of coordination of Natura 2000 site designation at the national level. We believe this study could be interesting for other (large) countries worldwide with similar de-centralisation of nature conservation administration.