Hybridisation and introgression are important processes influencing the genetic diversity and evolution of species. These processes are of particular importance in protected areas, where they can lead to the formation of hybrids between native and foreign species and may ultimately result in the loss of parental species from their natural range. Despite their importance, the contribution of hybridisation and introgression to genetic diversity in Sorbus genus remains not fully recognised. We analysed the genetic and morphological variability of several Sorbus species including native (Sorbus aria), foreign (S. intermedia) and potentially hybrid (S. carpatica) individuals from the Polish Carpathian range. Patterns of variation at 13 nuclear microsatellite loci show hybridisation between the tested species and confirm the existence of the hybrid form Sorbus carpatica. Biometric analysis on leaves, based of ten metric features and three parameters, identified several characters for preliminary taxonomic classification, however none of them could be used as a fully diagnostic marker for faultless annotation of Sorbus intermedia and S. carpatica. The genetic structure analysis indicated complex patterns of population differentiation and its diverse origin. The results allow assessment of genetic variation and identification of parental species participating in hybridisation. This knowledge will advance the management of genetic diversity and development of conservation strategies for efficient maintenance of the unique protected ecosystem.