Polymorphisms are widely known in allozymes and are often assumed neutral in the context of phylogenetic and population genetic analyses. However, several studies revealed that, in some loci and species, selection is strongly acting on allozymes and that temperature seems to be an important selective agent. Therefore, we individually determined the recovery time from chill-coma and heat knock-down time of 542 individuals of P. coridon sampled at four sites. Afterwards, we analyzed patterns of allozyme variations in these butterflies by allozyme electrophoresis of eleven loci to test the enzymes' performance under thermal stress conditions and to investigate the possibility of adaptive genotypic variation in relation to temperature stress resistance traits. We obtained significant differences of reactions to cold and heat shocks between the sexes and between reared and wild-captured individuals, but no significant differences among genotypes were found for most of the investigated allozyme loci. However, the Aat1 locus showed significant differences between different genotypes in chill-coma recovery times (p < 0.001), and marginal differences in heat knock-down times (p = 0.073). Thus, Aat1 might be a target for thermal selection. Consequently, our results revealed no clear influence of temperature on most allozyme loci and the otherwise observed differentiation in P. coridon might be explained by stochasticity, and thus geographic structuring should reflect biogeographic processes.