Recent phylogenetic studies have shown that Saxifraga, as currently understood, must be divided into two genera: Saxifraga L. sensu stricto and Micranthes Haw. To better understand the evolutionary history of these two genera, we performed phylogenetic analyses inferred from the nuclear ribosomal sequences from the internal transcribed spacer and the sequences of the plastid DNA (rbcL). Our molecular data confirmed the monophyly of the genus Micranthes and the consistency of the existing systematic treatments based on morphological criteria. Moreover, Micranthes species native from the Iberian Peninsula (i.e. M. clusii, M. lepismigena and M. stellaris) should be included into Micranthes sect. Arabisa.