AFLP and morphological data were used to reconstruct the phylogeny of Polylepis (Rosaceae). Results from the morphological analysis correlate well with earlier hypotheses about the evolution of the genus, showing a transition from tall, thin-leaved trees with large inflorescences to small trees with thick leaves and reduced inflorescences. While a basic phylogenetic signal is also discernible in the AFLP analysis, it is partly eclipsed in that samples from different species sometimes cluster according to geographic proximity rather than systematic affiliation. This structure is interpreted as indicative of frequent hybridization and introgression.