Aim The effects of glacial disjunctions on intraspecific differentiations are in the focus of phylogeographical studies. Several studies investigate the consequences of post-glacial expansions from glacial refugia on the composition within major genetic lineages.Location and methods We analysed the geographical pattern of allozyme variation of twenty loci of Polyommatus coridon (Poda, 1761) (Lepidoptera: Lycaenidae) from thirty-six localities spread throughout large regions of its European range. A total of 1566 individuals were analysed.Results We obtained a significant genetic differentiation (FST 0.060 ± 0.007). Further analyses showed a division into two major genetic lineages with a mean genetic distance (Nei, 1978) of 0.041 (± 0.010 SD). Applying an AMOVA, more than three quarters of the variance between populations was between these lineages and less than one quarter within these lineages. Both genetic lineages showed a significant decline in the number of alleles from southern to northern populations. Furthermore, we found a contact zone of these two major genetic lineages in eastern Central Europe extending throughout north-eastern Germany, then following the mountain regions along the Czech-German border and passing through the eastern Alps in a north–south direction.Main conclusions We assume that this differentiation evolved during the last ice-age as a result of isolation in the Adriato- and the Ponto-Mediterranean region. The loss of genetic diversity from the south to the north within both lineages reflects the decline of diversity during the post-glacial expansion.