Extreme arid conditions in the Atacama Desert in northern Chile have created a unique vegetation almost entirely restricted to the desert margins along the coast of the Pacific Ocean and the Andean range. In this study we provide data on the desert vegetation along elevational gradients at four localities from the western Andean slopes, between 19 degrees and 21 degrees S. Additionally, zonation of floristic data was explored. Three altitudinal zones could be classified and described in detail for each locality. Conspicuously divergent floras in the Atacama Desert have been recorded in the coastal lomas formations' and in the Andean desert vegetation, separated by a narrow band of absolute desert. In this study, we investigate the floristic relationships between both regions by implementing similarity analyses for 21 localities from the coastal and Andean deserts in northern Chile. Our results show a drastic east-west divergence in pairwise floristic similarity, which is in stark contrast to a weaker north-south divergence. A biotic barrier, preventing plant exchange from east to west and vice versa, imposed by the hyperarid conditions of the absolute desert, is one possible explanation for this finding. Moreover, the coastal and Andean deserts likely represent ecologically divergent habitats, e.g., in rainfall seasonality. Essential differences in factors determining plant life between both regions have probably contributed to a divergent evolution of the floras. Both explanations ecological divergence and ecogeographical isolation are not mutually exclusive, but likely complementary. We also combined floristic data from northern Chile and southern Peru. Similarity analyses of this combined dataset provide first floristic evidence for the existence of a biotic north-south corridor along the western slope of the Andes. Sub-Andean distributions of several species are discussed in the light of floristic connectivity between the Peruvian and Chilean Andean floristic clusters.