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In Arnica montana L. (Asteraceae) two subspecies are described, A. montana subsp. atlantica (AMA), present only on the Iberian Peninsula and A. montana subsp. montana (AMM) with a very wide distribution area. The morphological differences between the two subspecies are small and variable. Therefore, this concept is sometimes questioned. To establish the genetic background of the two subspecies, populations of AMA and AMM together with herbarium samples and DNA Bank material of AMM were tested with 12 microsatellite markers. A. montana propagates by seeds or by clonal propagation of its rhizome. In AMA, clonality was frequent while in AMM only one case of clonality could be identified. Therefore, further results were clone-corrected. Genetically, AMA separated very well from AMM with a G ST between the subspecies of 0.81, genetically justifying the subspecies concept of A. montana. Genetic variability in AMA (H exp =0.28) was lower than in the AMM populations (H exp =0.70). A somewhat higher fixation index of AMA (F ST = 0.17, compared to an F ST =0.08 for AMM) may indicate that geneflow in AMA is a bit more restricted than in alpine AMM. However, the fixation index of AMA is not deviating from Hardy-Weinberg equilibrium. No inbreeding was observed for AMA (F IS = 0.10) and AMM (F IS =0.08).