The dataset contains (1) a list, indicating the altitudinal distribution of species along four transects (Quebrada Aroma, Altos de Pica, Quebrada Blanca and Tambillo) and collection numbers of the 153 herbarium specimens. (2) A list of Literature used for the identification of recorded specimens. (3) presence/absence data of 615 plant species for 21 localities in northern Chile and southern Peru. (4) floristic and vegetation data along an elevational gradient for four study transects: Quebrada Aroma, Altos de Pica, Quebrada Blanca and Tambillo. Additional information regarding the plot setup is provided (values labeled with a minus sign indicate species recorded outside the actual study transects. ‘y’ indicates presence only without any information about abundance). (5) A list of species occurring in both, North Chilean Andean Desert and North Chilean Coastal Desert and additional information about their distribution. (6) A list of species occurring in the North Chilean Andean Desert and Peruvian Desert and additional information about their distribution.