Saxifraga pentadactylis subsp. almanzorii, an endemic to the subalpine nucleus of Sierra de Gredos (central Spain), differs from its closest relative, subsp. willkommiana, by its less showy petals. An artificial crossing program was carried out in order to assess the degree of reproductive isolation between the subspecies. To facilitate interpretation of the results, the program was extended to 10 other interspecific hybrid combinations within sect. Saxifraga. All the data gathered are congruent with the occurrence of two evolutionary scenarios. Interspecific crossings, rendering moderate to high seed‐set (in obtaining the F1), and vigorous but relatively sterile F1 offspring, reveal reproductive barriers at the level of the F1 fertility, probably originated as a byproduct of divergent evolution. In contrast, intraspecific crossings within S. pentadactylis resulted in seed‐set values lower than expected (in obtaining the F1), in a majority of weak non‐viable F1 offspring but also in a few fertile F1 hybrid specimens which were able to originate F2 offspring. This second pattern reveals reproductive barriers at the level of the F1 vitality, probably arisen in a quite abrupt fashion. The lower P/O for subsp. almanzorii as compared to subsp. willkommiana, together with the rest of the evidence suggest that the reproductive barriers between them might be the product of active selection against hybridization achieved by incrementing the levels of autogamy in the former.