Distribution areas of narrowly endemic species in the European Alps often coincide with Pleistocene refugia, suggesting that allopatric divergence due to Pleistocene range shifts might have been instrumental in their origin. Here, we infer the phylogenetic position of the locally endemic Doronicum cataractarum testing previous hypotheses with respect to its biogeographic and temporal origin (Tertiary origin with southwest Asian affinities versus possibly Pleistocene origin in the Alps). To this end, we extended existing genus-wide data sets of nuclear and plastid DNA sequences and obtained sequences from two hitherto not used low copy nuclear markers. These data sets were analyzed, as single markers and jointly in a concatenated matrix, using maximum parsimony and maximum likelihood. Temporal and spatial origins of D. cataractarum were inferred using mean path lengths and dispersal–vicariance analysis, respectively. Phylogenetic resolution was limited, but several geographically coherent groups were identified, including the Grandiflora group comprising southern and central European mountain species. Congruently, D. cataractarum was inferred as most closely related to Alpine species from the Grandiflora group (D. clusii, D. stiriacum and D. glaciale), but neither to southwest Asian species nor to European D. austriacum. The origin of D. cataractarum was conservatively dated to about 1.9 Mya and inferred to have taken place in the Alps. The striking morphological differences between D. cataractarum and the most closely related species likely are the result of adaptation to different habitats or, alternatively, the presence of plesiomorphic traits in D. cataractarum.