We studied the woody flora of seasonally dry forests in the middle section of the Urubamba river, Cusco region in southern Peru. We set up twenty 0.1 ha plots at altitudes between 700 and 1300 masl and enumerated all individuals with diameter at breast height (dbh) ≥ 2.5 cm. We recorded 5259 individuals belonging to 552 species, 303 genera and 82 families. On average, we recorded 92 species/plot, with a maximum of 150 species/plot. The most species rich families in the area were Fabaceae (69 species), Bignoniaceae (30), Moraceae (27), Apocynaceae (23) and Sapindaceae (22). The most species rich genera were Inga (13 species), Aspidosperma (11), Ficus (11), Machaerium (10) and Eugenia (9). The five most abundant species were Allophylus punctatus (142 individuals), Pogonopus tubulosus (122), Warszewiczia coccinea (111), Annona neoulei (106) and Anadenanthera colubrina (95). Multivariate floristic analyses suggested three types of dry forests in the area: Amazonian pluviseasonal tropical dry forest, sub-Andean pluviseasonal tropical dry forest, and savanna-like pluviseasonal tropical dry forest. A phytogeographical analysis showed that the dry forest in the Urubamba is more related to the dry forests in the Bolivian Chiquitania, than to other Peruvian dry forests. The conservation status of these forests is critical since much of their original area has been converted to other land use. We conclude that the high diversity of woody taxa and the phytogeographical relations suggest that the Urubamba dry forests are an Andean-Amazonian and neotropical dry forest hotspot, requiring urgent protection and conservation in the face of current rapid destruction.