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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 …