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The threatened European species Arnica montana L. is a plant much appreciated in the pharmaceutical industry, Galicia (North-Western Spain) being one of the main supply regions. Two chemotypes based on the content of sesquiterpene lactones have been found in this area: a chemotype dominated by helenalins, common in Central Europe, and another dominated by dihydrohelenalins, only found currently in Galicia. The aim of this work was to analyse the phylogenetic relationships and genetic diversity of Arnica montana in Galicia and their concordance with previous biochemical and environmental information. Two polymorphic chloroplast markers were sequenced in individuals from populations showing significant biochemical differences and situated in different environments (heathland, hay-meadow and peatland). Three haplotypes, different from those previously described in Europe, were found in Galicia and our results suggest that one of them could be ancestral inside the species. Significant population differentiation was detected in the studied area but genetic diversity within populations was low, only showing variability in heathland populations. This study is the first one describing the genetic diversity of Arnica montana in the extreme SW of Europe. The results suggested the presence of two different genetic groups (one of them ancestral) and were congruent with the two chemotypes described. Plants from heathlands displayed the highest variability because the two chemotypes were present in them. Future design of conservation and economical management plans for this threatened species should take into account this genetic variability and prioritize further genetic and chemical characterizations across the distribution range of the species.