1. We investigated the patterns of taxonomic and functional diversity of butterflies within the limits of the NATURA 2000 sites at two national parks, on the mountains Olympus and Rhodopes, in Greece. The study was conducted along an elevation gradient in 24 sampling sites on each mountain using the line transect technique.2. Species richness and abundance followed a monotonic decline on Olympus which is much higher, steeper and has a smaller area size, whereas there was no significant pattern on Rhodopes where average richness and abundance were highest at the extended mid-elevations with flatter landscape. The altitudinal zonation of butterfly communities on both mountains was primarily due to the specificity of some red-listed species to high elevations, as well as to the preference of common butterfly species for low or intermediate altitudes.3. Additive partitioning and null model analyses suggest an ecological redundancy on both mountains, as the environment is filtering species in terms of their environmental requirements rather than their functional position per se. Butterfly communities at high altitudes were not nested subsets of lowland communities. Environmental filtering led to the dominance of generalist species of which many were taxonomically close and had also similar life-history traits.4. The application of complementary networks showed that butterfly SPecies of European conservation Concern (SPEC) are good surrogates of the overall butterfly fauna on both mountains. Thus, our study highlights the importance of the conservation targeting of SPEC's especially at high elevations, where red-listed butterflies are more frequent and potentially threatened by climate change.