Mepraia is a genus (Triatominae) endemic to Chile and a vector of Trypanosoma cruzi. Alternative phylogeographic hypotheses have been suggested for Mepraia. We tested different colonization routes hypothesized using mitochondrial sequences and phylogeographic approaches to select the best-supported hypothesis. Our results suggest that, after the split from the sister genus Triatoma at ~4.3 Mya, Mepraia formed two main clades at ~2.1 Mya. The northern clade diverged from Mepraia sp. ~1.7 Mya, giving rise to M. parapatrica and M. gajardoi about ~1.4 Mya. The southern clade originated M. spinolai ~1.68 Mya. We suggest that Mepraia had an origin in the north-central Andes along with orogenic processes, reinforced by hyperaridity during the Pliocene. The hyperarid cycle would have separated the southern and northern clades. Then, in the northern clade, dispersal occurred north and south from the centre through corridors during the Pleistocene Climatic Oscillations. Climate changes may have induced a major speciation process in the Atacama Desert, while the more homogeneous habitat colonized by the southern clade led to only one, but structured, species.