Abstract Aim We used inferences of phylogenetic relationships and divergence times for three lineages of highland pitvipers to identify broad‐scale historical events that have shaped the evolutionary history of Middle American highland taxa, and to test previous hypotheses of Neotropical speciation. Location Middle America (Central America and Mexico). Methods We used 2306 base pairs of mitochondrial gene sequences from 178 individuals to estimate the phylogeny and divergence times of New World pitviper lineages, focusing on three genera ( Atropoides , Bothriechis and Cerrophidion ) that are broadly co‐distributed across Middle American highlands. Results We found strong correspondence across three highland lineages for temporally and geographically coincident divergences in the Miocene and Pliocene, and further identified widespread within‐species divergences across multiple lineages that occurred in the early–middle Pleistocene. Main conclusions Available data suggest that there were at least three major historical events in Middle America that had broad impacts on species divergence and lineage diversification among highland taxa. In addition, we find widespread within‐species genetic structure that may be attributable to the climatic changes that affected gene flow among highland taxa during the middle–late Pleistocene.