We analysed the variation at mitochondrial DNA (mtDNA) and six allozyme loci in two transects across a hybrid zone between the fire-bellied toads Bombina bombina and Bombina variegata in southern Poland. The mtDNA cline was narrower than allozyme clines in one transect (Przemyśl, β = 0.435, w = 3.42 km) and shifted to the B. bombina side in both (near Kraków by 1.32 km, α = 0.437, and near Przemyśl by 0.97 km, α = 0.319). Cytonuclear associations were weak. Narrowed mtDNA clines could be a by-product of female demography and lowered effective population size of mtDNA. Alternatively, restricted mtDNA introgression is a likely result of negative epistasis in recombinants augmented by environment-dependent selection because divergence of Bombina mitochondrial and nuclear genomes is large. The shift of the mtDNA cline, contrary to expectations from initial mating preferences and fecundity differences between the species, suggests that on the B. bombina side of the zone hybrid females with B. variegata mtDNA have a higher chance of leaving progeny. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 295–306.