The narrow Strait of Gibraltar has separated the African and European continents since the Miocene (5.3 Mya), with a different degree of permeability for Mediterranean taxa. Southern and northern regions of the Iberian Peninsula and Morocco, respectively, are key areas to evaluate the colonization dynamics and biogeographic history of taxa occurring at both sides of this strait. The Ibero-Maghrebian subspecies of the European pond turtle, Emys orbicularis occidentalis, is patchily distributed and threatened throughout most of the Iberian Peninsula and northern Morocco and its origin is thought to be in North Africa. Here we expand the geographic sampling across the Iberian Peninsula and Morocco, with special emphasis in the southern tip of the peninsula and northern Morocco, and analyze mtDNA sequences of 183 E. o. occidentalis to better understand the complex biogeographic history of this subspecies. We provide for the first time evidence for shared haplotypes of Iberian and North African pond turtles, with an additional haplotype in the southern Iberian Peninsula derived from Moroccan haplotypes. This supports the hypothesis that the Strait of Gibraltar constitutes no significant biogeographic barrier for E. orbicularis. However, the newly discovered shared, or extremely similar, haplotypes of European pond turtles from the southern Iberian Peninsula and Morocco suggest either that at least two independent natural colonization waves from Morocco have reached the Iberian Peninsula or that Moroccan turtles were accidentally or deliberately introduced there.