Aim: To test hypotheses on the origin and assembly of the flora of the Chihuahuan Desert using as a system the hard-leaved shrubby lineages of the Rosaceae distributed in North American Deserts. Location: North American Deserts, Chihuahuan Desert, Mexican Plateau, Tehuacan Valley. Taxa: Rosaceae, Amygdaloideae (Amelanchier paniculata, Lindleya mespiloides, Malacomeles denticulata, Vauquelinia angustifolia, Vauquelinia australis, Vauquelinia corymbosa, Xerospiraea hartwegiana), Dryadoideae (Cercocarpus fothergilloides, Cercocarpus pringlei, Cercocarpus rzedowskii, Purshia plicata) Methods: Phylogenetic analyses were conducted based on nine chloroplast and nuclear molecular markers of eleven newly sequenced species of Rosaceae distributed in the Chihuahuan Desert along with previous sequences of 41 species in 25 genera representative of the major clades in the family. Based on phylogeny, divergence times, migration, vicariance events and ancestral biogeographic areas were determined. Ecological niche-based modelling will predict changes in distribution during Pleistocene climate oscillations. Traitgrams were constructed to visualize departure among lineages in the most significant climate variables. Results: The lineages studied diverged during the Eocene-Oligocene (53-33 Mya). The ancestral area for most of the taxa was in the Mojave and Chihuahuan Deserts. Most dispersal events occurred from the Mojave Desert to the central area of the Chihuahuan Desert on the Mexican Plateau. Ecological niche-based modelling suggests a contraction of suitable habitat during the Last Interglacial period (similar to 120,000-140,000 years), followed by expansion during the Last Glacial Maximum (similar to 22,000 years) and the Middle Holocene (similar to 6,000 years). Main conclusions: Our results confirm the Axelrod's hypothesis of an origin of the flora of the Chihuahuan Desert in SW North America migrating to occupy North American arid lands. Vicariance and the expansion of arid lands allowed divergence, migration and permanence of the lineages studied on the Mexican Plateau. Divergence occurred prior to the onset of aridification. The Mexican Plateau acted as a refuge for hard-leaved lineages during the Miocene. Shifts in ecological niches of related species allowed them to colonize new areas with different temperatures and precipitation. Current distribution of lineages is the most limited.