Background and aims Jurinea pinnata is an Iberian vascular plant which only grows on gypsum and dolomite, two types of rocks associated with their exclusive endemic floras. In addition, the plant has an island-like distribution which could affect the differentiation and the genetic variability of wild populations. Thus, the species provides a unique opportunity for comparing (bio) geographical and ecological (edaphic) differentiation by means of molecular markers. Methods For our investigation we took 24 soil samples paired with a similar number of foliar samples for nutritional analyses. Our molecular-marker approach (AFLPs) involved 16 populations. Results The edaphic parameters revealed significant dissimilarities between dolomitic and gypsum soils. These differences are also found in the mineral composition of the leaves. However, molecular data revealed that the differentiation between populations correlates better with geographical isolation than with the substrate character. Conclusions The populations showing the greatest genetic diversity are those of the East Baetic territory where the species grow on both substrates and its populations are closer together. The plant tolerance to gypsum and dolomite can be explained either as a result of common adaptive mechanisms or of a more general adaptation to arid environments.