In this study, we report species diversity and endemism of the poorly known but highly diverse Seasonally Dry Tropical Forest (SDTF) flora of the Marañón valley in northern Peru. We characterise woody vascular plant species diversity across the valley in order to define the conservation value of the area at national and international level. Based on 32 rapid botanical inventories, 92 plots of 50 × 20 m, and a herbarium study across local and international herbaria, we report 440 woody vascular plant species of which 143 (33%) are endemic to the valley. Two centres of endemism within the valley are identified, each with clear elevational zonation of diversity. Data show that the Marañón valley is a good representative of Peruvian SDTFs as a whole, with an average of 56% SDTF species and 78% SDTF genera found in the one valley. The results show that there is wide variation in the set of dominant species across the valley, and that many local endemics are locally abundant unlike in neighbouring SDTFs where the dominant species are all geographically widespread. Our results demonstrate that the Marañón includes a rare combination of both nationally representative yet globally unique plant species, which makes the valley an ideal conservation target. The high level of endemism structured within elevational zones implies that conservation areas should be established across elevational zones in order to maximise the protection of this globally unique flora.