The dataset contains floristic data and a literature database from the Atacama and Peruvian Desert and includes the following files: S1 Table. Altitudinal distribution range of species within the four studied transects indicating lowest (min) and highest (max) elevation of each species along each transect. S2 Table. Literature used for the identification of specimens recorded along the four studied transects in a ris-format. S3 Table. Working table including presence/ absence data of 615 species for 21 localities in northern Chile and southern Peru. S4 Table. Working table including altitudinal vegetation and floristic data assessed along the four studied transects. Values labelled with ‘-‘ indicate species recorded outside the actual studied transects. S5 Table. Distribution ranges of species found in the North Chilean Andean Desert and North Chilean Coastal Desert cluster. S6 Table. Distribution ranges of species found in the Peruvian Desert and in the North Chilean Andean Desert cluster. The tables S1, S3-S6 are available in Excel-Format as well as .csv files.