Weberbauera (Brassicaceae, tribe Thelypodieae) comprises 18 species distributed along the central Andes of Argentina, Bolivia, Chile and Peru. Of these species, W. spathulifolia has the largest geographical range in the genus, extending c. 3000 km along the Andean highlands from La Rioja Province in Argentina to Ancash Department in Peru. This species also shows the greatest morphological variation in the genus. However, whether this geographical and morphological variation represents one or more lineages remains unclear. In this study, we analyse W. spathulifolia across its entire distribution range using molecular, morphological and ecological data. Because there is no phylogenetic analysis for the genus, we generated a comprehensive molecular sampling using nuclear (ITS) and plastid (trnL-F and trnH-psbA) sequences for other Weberbauera spp. and representatives of South American Thelypodieae. Results support the presence of two different lineages within W. spathulifolia, one in the northern part of the species range and the other distributed across its southern and central range. In addition to the morphological differences and the allopatric distribution, these lineages also differ in their climatic niches. Therefore, we propose here to retain the northern lineage under W. spathulifolia and to treat the southern-central lineage under W. orophila, comb. nov. Phylogenetic placement of Weberbauera spp. among the South American Thelypodieae is also analysed and discussed. Results of this study contribute to understanding the biodiversity and evolution of the Andean Brassicaceae.