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The phylogeography of ‘southern’ species is relatively well studied in Europe. However, there are few data about ‘northern’ species, and so we studied the population genetic structure of the arctic-alpine distributed burnet moth Zygaena exulans as an exemplar. The allozymes of 209 individuals from seven populations (two from the Pyrenees, five from the Alps) were studied by electrophoresis. All 15 analysed loci were polymorphic. The mean genetic diversities were moderately high ( A: 1.99; He: 11.5; P: 65%). Mean genetic diversities were significantly higher in the Alps than in the Pyrenees in all cases. FST was 5.4% and FIS was 10%. Genetic distances were generally low with a mean of 0.022 between large populations. About 62% of the variance between populations was between the Alps and the Pyrenees. The two samples from the Pyrenees had no significant differentiation, whereas significant differentiation was detected between the populations from the Alps ( FST = 2.8%, P = 0.02). Zygaena exulans had a continuous distribution between the Alps and the Pyrenees during the last ice age. Most probably, the species was not present in Iberia, and the samples from the Pyrenees are derived from the southern edge of the glacial distribution area and thus became genetically impoverished. Post-glacial isolation in Alps and Pyrenees has resulted in a weak genetic differentiation between these two disjunct high mountain systems. [ABSTRACT FROM AUTHOR]