The importance of the Mediterranean Basin as a long-term reservoir of biological diversity has been widely recognized, although much less effort has been devoted to understanding processes that allow species to persist in this area. Ramonda myconi (Gesneriaceae) is a Tertiary relict plant species restricted to the NE Iberian Peninsula. We used RAPD and chloroplast markers to assess the patterns of genetic structure in eight mountain regions covering almost the full species range, to identify the main historical processes that have shaped its current distribution and to infer the number and location of putative glacial refugia. While no cpDNA variation was detected, the species had relatively high levels of RAPD variation. Maximum levels of diversity were found within populations (71%), but there was also a significant differentiation between geographical regions (20%) and among populations within regions (9%). A spatial AMOVA identified three main groups of populations, corresponding to previously recognized centers of endemism and species richness. In addition, we found a marked geographical pattern of decreasing genetic diversity and increasing population differentiation from west to east. Our results support a complex phylogeographic scenario in the Iberian Peninsula of "refugia-within-refugia" and suggest that the higher diversity observed in western regions might be associated with prolonged and more stable climatic conditions in this area during the Quaternary.