During the post-glacial warming, cold-adapted species shifted their distribution to higher latitudes and altitudes and became widely extinct over the European lowlands. The butterfly Lycaena helle shows this feature, and is currently distributed in highly isolated habitat remnants restricted to higher elevations over Central Europe. We analysed five polymorphic microsatellite loci and applied Climate Envelope Modelling. We detected strong genetic differentiation coinciding with the orographic structures of seven distinct mountain regions. This picture become underlined by deflecting levels of genetic diversity and the presence of private alleles, endemic for each single mountain area. Furthermore, genetic differentiation among populations within these mountain groups were detectable and reveal interrupted geneflow on a regional level. This genetic picture of a fragmented distribution coincides with the obtained pattern of potential suitable habitats given by a Climate Envelope Model. A scenario of further climate warming predicts a loss of the major parts of these areas and rising fragmentation of the remainings. The predicted extinction of some populations will cause the loss of unique alleles, which are recently restricted to the given populations.