The Andes are the most species-rich global biodiversity hotspot. Most research and conservation attention in the Andes has focused on biomes such as rain forest, cloud forest, and páramo, where much plant species diversity is the hypothesized result of rapid speciation associated with the recent Andean orogeny. In contrast to these mesic biomes, we present evidence for a different, older diversification history in seasonally dry tropical forests (SDTF) occupying rain-shadowed inter-Andean valleys. High DNA sequence divergence in Cyathostegia mathewsii, a shrub endemic to interAndean SDTF, indicates isolation for at least 5 million years of populations separated by only ca. 600 km of high cordillera in Peru. In conjunction with fossil evidence indicating the presence of SDTF in the Andes in the late Miocene, our data suggest that the disjunct small valley pockets of inter-Andean SDTF have persisted over millions of years. These forests are rich in endemic species but massively impacted, and merit better representation in future plans for science and conservation in Andean countries.biogeography | dispersal limitation | Neotropics | phylogenetic niche conservatism | phylogeography G eotemporal patterns of historical species assembly in the world's biodiversity hotspots and especially in species-rich tropical biomes are poorly understood. Many questions remain to be answered about how the biota of biodiversity hotspots were assembled and how comparable different hotspots are. To gain insights into these questions, we investigate plant species diversification in the tropical Andes, which contain ca. 40,000 plant species, ≈15% of the global total, in only 1% of the world's land area. Most of this diversity is found in the lowland and midelevation mesic forests of the Andean flanks. The "excess" of species in these forests largely explains why the Neotropics contain more plant species than both tropical Africa and Asia, and was hypothesized by Gentry (1, 2) to have been produced by recent, rapid species diversification coinciding with the accelerated orogeny of the Andes over the past 10 million years. Gentry's recent-species diversification model has received support from several dated phylogenies of plant clades with distributions