Phylogeographic studies during the last decade confirmed an internal complexity of the Iberian Peninsula and northern Maghreb as refugial areas during the Miocene to Pleistocene period. Species with low vagility that experienced the complex climatic and palaeogeographic processes occurred in the Western Mediterranean Basin are excellent candidates to study the extent of lineage diversification in this region. We applied phylogenetic analyses based on mitochondrial data to infer the evolutionary history of Vipera latastei/monticola and identify the major biogeographic events structuring the genetic diversity within this group. We obtained a well-resolved phylogeny, with four highly divergent lineages (one African and three Iberian) that originated in the Tertiary. Coalescence-based estimations suggest that the differentiation of the four major lineages in V. latastei/monticola corresponds to the Messinian salinity crisis and the reopening of the Strait of Gibraltar during the Miocene. Subsequent Pliocene and Pleistocene climatic oscillations continued to isolate both Iberian and Maghrebian populations and led to a high genetic structuring in this group, particularly in Southern Iberia, a complex palaeogeographic and topographic region with high endemism levels. This study does not support the current taxonomy of the group, thus suggesting that an integrative evaluation of Iberian and African populations is needed to resolve its systematics.