The implementation of biodiversity studies to set conservation priorities assumes that the different criteria used in prioritisation are correlated. Based on butterfly data, we examined whether high total diversity (species density and richness), unique species assemblages, and high numbers of different categories of Species of European Conservation Concern (SPEC) were co-located in the same habitats in the Picos de Europa National Park, Spain. Species density (number of species per sample) declined with elevation and was significantly higher in Genista shrublands on southern slopes (Southern Genista shrubland). We found unique species assemblages for Southern Genista shrublands, heathlands, mown meadows and subalpine meadows, whereas Genista shrubland on northern slopes (Northern Genista shrubland) and pastures were occupied by more habitat generalist species. We also found an effect of elevation on species composition. Species with global distributions concentrated in Europe (SPECs 4b) tended to be associated with Southern Genista shrubland, whereas species with global distributions restricted to Europe (SPECs 4a) were associated with higher elevations. Thus, we suggest a higher conservation value for butterfly assemblages located both on Southern Genista shrublands and at high elevations as they contain unique assemblages with a higher number of SPECs. By comparing our data with a previous study on carabid beetles, we found a low coincidence between butterflies and beetles for habitats with high species diversity and unique assemblages. Our study suggests that preserving areas in the landscape supporting higher butterfly diversity only partially preserves those species of greater conservation concern, and that butterflies cannot be used as a reliable indicator of other priority taxa for conservation, such as carabid beetles.