The Andean Lupinus radiation presents one of the highest rates of net species diversification in plants and includes species with a wide variety of growth forms, but the detailed geographical and adaptive trajectories of diversification in the Andes remain unresolved. One of the most distinctive of these growth forms is the fistulose-inflorescence rosette, FIR, typical of tropical high-elevation habitats. To gain insights into the evolutionary origins of this growth form and the biogeography of Andean Lupinus, genome-scale nextRADseq data were generated for 124 individuals from the northern and central Andes. The RADseq data provide unprecedented phylogenetic resolution among the recently diverged Andean Lupinus spp. and suggest multiple independent evolutionary origins of the rosette growth form and marked geographical structure across the northern Andes at different scales. This suggests that both adaptive (ecological) and geographically driven non-adaptive diversification have contributed to rapid recent species diversification. Among the north-Andean FIR Lupinus spp., our results strongly support recognition of L. alopecuroides (Central Cordillera and northern Ecuador), L. triananus (southern portion of the Eastern Cordillera) and a putative new species from the ‘Pisba-Cocuy’ and ‘Ocetá’ páramos (northern portion of the Eastern Cordillera).