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Premise: The cactus family (Cactaceae) is a speciose lineage with an almost entirely New World distribution. The genus Eulychnia with eight currently recognized species is endemic to the Atacama and Peruvian Deserts. Here we investigated the phylogeny of this group based on a complete taxon sampling to elucidate species delimitation and biogeographic history of the genus. Methods: A family‐wide Bayesian molecular clock dating based on plastid sequence data was conducted to estimate the age of Eulychnia and its divergence from its sister genus Austrocactus. A second data set obtained from genotyping by sequencing (GBS) was analyzed, using the family‐wide age estimate as a secondary calibration to date the GBS phylogeny using a penalized likelihood approach. Ancestral ranges were inferred employing the dispersal extinction cladogenesis approach. Results: Our GBS phylogeny of Eulychnia was fully resolved with high support values nearly throughout the phylogeny. The split from Austrocactus occurred in the late Miocene, and Eulychnia diversified during the early Quaternary. Three lineages were retrieved: Eulychnia ritteri from Peru is sister to all Chilean species, which in turn fall into two sister clades of three and four species, respectively. Diversification in the Chilean clades started in the early Pleistocene. Eulychnia likely originated at the coastal range of its distribution and colonized inland locations several times. Conclusions: Diversification of Eulychnia during the Pleistocene coincides with long periods of hyperaridity alternated with pluvial phases. Hyperaridity caused habitat fragmentation, ultimately leading to speciation and resulting in the current allopatric distribution of taxa. [ABSTRACT FROM AUTHOR]