Mesoclemmys dahliandM. zuliaeare two endangered, little-known toad-headed turtles with small distribution ranges in Colombia and Venezuela, respectively. Using the mitochondrial cytochromebgene as a marker, we investigate their phylogeographic differentiation. Furthermore, based on 2341 bp of mtDNA and 2109 bp of nDNA ofM. dahli,M. zuliaeand allied chelid turtles, we infer their divergence time using a fossil-calibrated relaxed molecular clock approach.Mesoclemmys dahliandM. zuliaeare closely related species, with an estimated mean divergence time of 10.6 million years. This estimate correlates with the uplift of the Serranía de Perijá, an Andean mountain chain separating their distribution ranges, suggesting that this event could have caused the evolution of the two species. Haplotype and nucleotide diversities ofM. dahliare markedly higher than inPodocnemis lewyana, another endemic turtle species of Colombia. This pronounced dissimilarity may reflect differences in the phylogeographies and demographic histories of the two species, but also different habitat preferences.