Iberian populations of Arnica montana L. (Asteraceae) represent a valuable resource both for conservation and pharmaceutical industry. Previous genetic analyses pointed out the presence of different genetic groups, but a wide region is still genetically unexplored. In order to fill this scientific gap, the present study analysed a wider sampling area along the northern Iberian Peninsula. Nuclear (i.e. microsatellite loci) and plastid DNA (cpDNA) molecular markers were used to assess the levels of genetic diversity and the population structure in 16 locations, eight analysed for the first time in the present study and eight representative of the different genetic groups previously identified. The two divergent cpDNA groups previously described were found, but their distribution was extended and refined. Thus, one of the groups (suggested as ancestral) was predominantly distributed in adjacent zones of the Cantabrian coasts while the other (more related to Central-European populations) was predominant in inner Cantabrian regions and Pyrenees. Genetic diversity with microsatellite loci (He = 0.280) was in accordance with the figures previously described, with a high level of population differentiation (FST > 0.500) identifying the presence of up to five population genetic units. Genetic and geographical distances were not related (no isolation-by-distance pattern identified), suggesting an important effect of genetic drift. Finally, due to the conservation and evolutionary interest of the populations analysed, different management actions useful for the maintenance of wild A. montana resources are provided.