Erodium paularense Fern. Gonz. & Izco (Geraniaceae) is a perennial, narrow endemic species of central Spain. Recently, three new populations have been found 160 km northwest of the first site, although the taxonomic status of the new populations has not yet been published. Random amplified polymorphic DNA (RAPD) markers were used to confirm that the new populations belong to E. paularense, and to evaluate the genetic diversity among individuals, populations and regions. The two regions were clearly differentiated through upgma, whereas significant φST distances between all pairs of populations were obtained by amova. Genetic distances between populations were partially explained by geographical distances. The clear genetic differentiation among regions, on top of the geographical distance and differences in geological substratum, supports a taxonomical discrimination of the regions at a subspecific level.