Rising temperatures and agricultural changes (intensification and succession on fallow land) during the last few decades have caused a strong decline of moist and cool sites on nutrient-poor grasslands and species depending on these habitats. We tested the effects of habitat deterioration on a local and regional scale in such a species, the highly endangered butterfly Lycaena helle, which was more widely distributed over central Europe during the postglacial period, but has recently become restricted to some remnants. We analysed five polymorphic microsatellite loci in 220 individuals sampled at ten different localities. The study sites in Germany, Luxembourg and Belgium are geographically split into three mountain regions: the Ardennes, the Eifel and the Westerwald; the latter is separated from the other two by the river Rhine. A comparatively high genetic diversity was detected in all local populations and genetic differentiation was found among the Ardennes, the Eifel and the Westerwald (F _CT: 0.084). The genetic differentiation among all populations (F _ST: 0.137) underlines natural and anthropogenic habitat fragmentation. While ongoing gene flow seems to exist among the Eifel populations indicating the only intact metapopulation, a high genetic differentiation in the Ardennes and the Westerwald indicates a disruption of population connectivity. Our genetic data obtained on different spatial scales show the genetic consequence of long-term isolation and should trigger necessary conservation measures at the metapopulation level.