The structure and geographic location of hybrid zones change through time. Current patterns result from present and historical population-environment interactions that act on each of the hybridizing taxa. This is particularly evident for species involved in complex hybrid zones, such as that formed by the toad species Bombina bombina and Bombina variegata (Anura: Discoglossidae), which interact along extensive areas in Central Europe. We used data on external morphology and partial sequences of the cytochrome oxidase I (cox1) and nicotinamide adenine dinucleotid dehydrogenase subunit 4 (nad4) mitochondrial DNA (mt-DNA) genes to analyze the current patterns of genetic structure shown by both species of Bombina along their contact zone in Hungary. Phylogenetic, phylogeographic, and historical demography analyses were applied to 1.5kb mt-DNA obtained from 119 individuals representing 24 populations from Hungary and additional specimens from Slovakia, Albania, and Bosnia-Herzegovina. We use these data to infer the evolutionary history of the isolated populations of B. variegata in Hungary and to discriminate between competing biogeographic scenarios accounting for the historical interactions between species in this region. Results from the inferred phylogenetic branching pattern and sequence divergence among species and populations support the following: (i) recent population expansion has occurred in Hungarian populations of B. bombina, which are genetically very homogeneous; (ii) the Hungarian populations of B. variegata correspond to two distinct mitochondrial lineages (Carpathian and Alpine, respectively); average maximum-likelihood-corrected sequence divergence between these lineages is 8.96% for cox1 and 10.85% for nad4; (iii) mt-DNA divergence among the three isolated western populations of B. variegata from Transdanubia is low, with four closely related haplotypes, which suggests that the isolation between these populations is the result of a recent process, possibly mediated by the invasion of B. bombina; and (iv) we have detected discordances between morphology and mt-DNA data in the Transdanubia region (Bakony Mountains, Mecsek Mountains, Orség area), suggesting mt-DNA introgression across species in this regions. These results are discussed with reference to previous biogeographic hypotheses.