A morphological survey and assessment of genetic diversity using amplified fragment length polymorphism (AFLP) were applied to study the variability of two agamospermous species of Hieracium section Cernua R. Uechtr. characterized by disjunct, subalpine distributions: H. silesiacum (Western Carpathians and Eastern Sudetes) and H. vierhapperi (Western Carpathians and Eastern Alps). Contrasting patterns were revealed. In H. silesiacum, no genetic or morphological differences were found between its remote populations from the Sudetes and the Tatry mountains, suggesting a recent dispersal. In contrast, distinct morphological differentiation of population in the Nízke Tatry mountains was confirmed by high genetic differentiation; the analysis indicated independent origin of this population and gave grounds for taxonomic separation and description of a new species, H. austrotatricum. In H. vierhapperi, genetic differentiation and slight morphological difference (colour of achenes) was observed between disjunct populations from the Carpathians and the Alps. The data suggest long-term isolation of these populations resulting in pronounced independent history. High number of markers monomorphic for all populations supports the existing hypothesis of common sexual ancestors from H. section Cernua involved in the origin of these polyploid taxa. No or only minor morphological differentiation within the taxa indicates high stability of apomictic populations of Hieracium. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 93–105.