Little is known of the direct effects of Quaternary glaciationdeglaciation cycles in plants within southern European refugia. This study, centered in the Sierra Nevada (S Spain), used RAPD and morphometric data from 36 populations of Armeria (Plumbaginaceae) from five taxa belonging to three species that are endemic to that region: A. filicaulis subsp. nevadensis, A. fili caulis subsp. trevenqueana, A. filicaulis subsp. alfacarensis, A. splendens, and A. villosa subsp. bernisii. The results based on genetic analyses at the population level (AMOVA, genetic diversity, genetic distance) and genetic and morphological analyses at individual level (haplotype phenetic distance, PCO, morphometrics) indicate that: (1) genetic diversity decreases with altitude, probably as a result of the postglacial recolonization processes, except in some secondary contact zones between taxa; (2) gene flow among interspecific populations, most likely facilitated by contraction of vegetation belts, led to the formation of hybrid taxa; (3) genetic distances among populations provide a useful basis for studying scenarios with frequent interspecific gene-flow since it allows distinguishing eventual cases of introgression from hybridogenous taxa.