The Andean tree genus Polylepis (Rosaceae) is notorious for the high morphological plasticity of its species and the difficulty in their circumscription. The evolutionary mechanisms that have driven diversification of the genus are still poorly understood, with factors as diverse as ecological specialisation, reticulate evolution, polyploidisation and apomixis being proposed to contribute. In the present study, chromosome counts, flow cytometry and stomata guard cell size measurements were employed to document for the first time the presence of polyploidy in the genus and to infer ploidy levels for most species. Inferred ploidy levels show a clear progression from diploidy in cloud forest species to polyploidy (tetra- to octoploidy) in the morphologically and ecologically specialised incana group, indicating that polyploidisation may have played a major role in speciation processes and the colonisation of novel habitats during the Andean uplift. At least two species of Polylepis comprise populations with varying degrees of ploidy. More extensive studies are needed to obtain a better understanding of the prevalence and effects of intraspecific polyploidy in the genus.