We used partial sequences of the cytochrome b mitochondrial DNA (mtDNA) gene, obtained from 76 individuals representing 45 populations of Iberian Salamandra salamandra plus 15 sequences of additional species of Salamandra and related genera, to investigate contact zones. These zones, identified by earlier allozymic and morphological analyses, are between populations of viviparous (S. s. bernardezi and S. s. fastuosa) and ovoviviparous (S. s. gallaica and S. s. terrestris) salamanders. The distribution of mtDNA and nuclear markers is mostly concordant at one contact zone (between S. s. gallaica and S. s. bernardezi), but at another (between S. s. fastuosa and S. s. terrestris) the markers are offset by about 250 km. The observed geographic variation fits a model of mtDNA capture. Among the potential mechanisms responsible for such discordance we favor a combination of range shifts due to climatic fluctuations and biased genetic admixture across moving contact zones. We apply our findings to the issue of possible homoplasy in the evolution of viviparity and conclude that viviparity likely arose only once within S. salamandra.