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Among the questions surrounding the biogeographical history of the Chilean biota, none has gathered more interest than the origin of the Fray Jorge (FJ) forest relict and its biota. Inserted in a semi-desert area, this forest enclave exists due to the existence of a very particular microclimate in this region. The age of the disjunction and the historical relationship between the FJ biota with the remaining components of South America are explained by two distinct, competing hypotheses: the first suggests that it would have become isolated during the climatic changes of the Paleogene/Neogene, while the second suggests that the isolation is a product of Quaternary glaciations. To discriminate between these competing hypotheses, we used DNA sequence phylogeny methods and molecular genetic dating to the study of a genus of land snails (Plectostylus) that occurs in the FJ relict and throughout Chile. The phylogeny shows a clear distinction between forest and arid clades, and each of these clades is formed by many geographically circumscribed populations. The FJ fragment snails form a clade that is sister to all other forest clades. The separation between the Fray Jorge clade and the other forest clades dates back to the Paleogene/Neogene. Our data suggest that the FJ forest is a relict from the forests that occupied that landscape during the Paleogene/Neogene and retreated due to the aridification of the region. We also observe that the current taxonomy of the Plectostylus genus must be re-evaluated.