The biodiversity hotspot of the Equatorial Pacific region in western Ecuador and northwestern Peru comprises the most extensive seasonally dry forest formations west of the Andes. Based on a recently assembled checklist of the woody plants occurring in this region, we analysed their geographical and altitudinal distribution patterns. The montane seasonally dry forest region (at an altitude between 1,000 and 1,100 m, and the smallest in terms of area) was outstanding in terms of total species richness and number of endemics. The extensive seasonally dry forest formations in the Ecuadorean and Peruvian lowlands and hills (i.e., forests below 500 m altitude) were comparatively much more species poor. It is remarkable though, that there were so many fewer collections in the Peruvian departments and Ecuadorean provinces with substantial mountainous areas, such as Cajamarca and Loja, respectively, indicating that these places have a potentially higher number of species. We estimate that some form of protected area (at country, state or private level) is currently conserving only 5% of the approximately 55,000 km2 of remaining SDF in the region, and many of these areas protect vegetation at altitudes below 500 m altitude. In contrast, the more diverse seasonally dry forests in mountainous areas remain little protected.