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We used multilocus phylogeographic analyses, morphometric measurements, and environmental niche models (ENMs) to analyze the recent evolution of the golden vireo Vireo hypochryseus, a Mexican endemic species. Vireo hypochryseus is made up of two phylogeographically structured mitochondrial DNA clades that probably diverged 132 000 yr ago. One clade comprised individuals from mainland Sinaloa and the Tres Marías islands in the northwest, and the other included individuals from the remaining range of the species. This marked phylogeographic structure contrasts with the low genetic structure reported for temperate North American vireos. The nuclear DNA markers also showed some geographic differences in allele frequency, but did not exhibit a clear phylogeographic structure. The morphometric analyses suggested a decreasing north to south cline, with the largest individuals located in the Tres Marías islands. The ENMs did not support a scenario of geographic fragmentation of the environmental conditions of the area in which V. hypochryseus has inhabited over the last 130 000 yr. However, a model of isolation by resistance based on the actual configuration of climatic conditions in western Mexico did explain a major proportion of both the mitochondrial DNA distances and the differences in size, while a model of isolation by distance explain a low proportion of such differences. Therefore, the recent history of V. hypochryseus was likely shaped by historical habitat fragmentation due to fluctuating environmental conditions in the mainland that produced a phylogeographic print, and natural selection on morphological traits in the insular population, suggesting an active diversification of endemic lineages in the Mexican dry forest.