Aim: The history of Agave lechuguilla, a characteristic and dominant plant of the Chihuahuan Desert, was reconstructed in order to determine the importance of the Neogene orogenic uplift and the Quaternary glacial-interglacial climatic changes on the genetic patterns of a native Chihuahuan Desert species. Location: Chihuahuan Desert, Mexico and United States. Methods: Chloroplast DNA data from A. lechuguilla were analysed to describe levels of genetic diversity and structure and to infer the species' demographic history, using traditional methods and approximate Bayesian computation (ABC). The time of divergence of the different haplogroups was estimated with a Bayesian approach. In addition, ecological niche modelling was used to identify possible refugia. Results: Molecular dating analyses showed that A. lechuguilla originated 4.46 Ma and later differentiated into four haplogroups. The average chloroplast genetic diversity was low (Hd, 0.24), with high levels of genetic differentiation (GST, 0.780). Demographic analysis, niche modelling and ABC indicated a recent expansion from at least five glacial refugia located south of the species' current distribution. Main conclusion: Agave lechuguilla originated in the Neogene, and the glacial-interglacial events of the Pleistocene resulted in the expansion and contraction of its range, playing an important role in its intraspecific diversification. These contraction-expansion events are consistent with biogeographical regions previously identified in the Chihuahuan Desert.