While Bufo bufo is widespread in Europe, the closely related B. spinosus is parapatrically distributed in Western Europe and Northern Africa. The exact course of the contact zone between both taxa, however, is still unknown. 24 samples from Switzerland were analysed using mitochondrial and nuclear markers combined with 243 previously published samples from Europe and Asia. No haplotypes of B. spinosus were detected in Switzerland, only two mitochondrial haplotypes of B. bufo: one north and south of the Alps, the other only north of the Alps. Both haplotypes are also widely distributed in Eastern and Central Europe. These results agree with a postglacial recolonisation of Central Europe from refugia on the Balkan Peninsula. The occurrence of one haplotype north and south of the Alps can be explained by colonisation either from the north by crossing the Alps or from the east along the southern edge of the Alps. The rapid postglacial recolonisation from Balkan refugia might have prevented the spread of southern haplotypes from Italy and of B. spinosus from France.