2. Using the software STRUCTURE 2.2, we found two distinct genotype clusters present in different frequencies at all study sites. The frequencies of these genotypic clusters varied significantly between years within the same site. Remarkably few individuals were of mixed ancestry, indicating that some isolating mechanisms are present. Twenty-seven mtDNA haplotypes were identified but they showed no geographic structure, nor were they related to either of the two genotype clusters identified in the AFLP data. 3. Most field observations of migrating red admirals suggest a regular north-south migration pattern in Europe. Our data indicate both long-distance migration and a more variable pattern in orientation, since the composition of the two genotypic clusters shows dramatic variation between sites and years in the northern part of the distribution range.