Both morphological and molecular-genetic marker analyses were used to identify the valuable populations in order to conserve the present-day gene pool of the wild roses in Europe. Therefore we aimed to expand the knowledge of the taxonomical complexity within the subgenus Rosa, especially within the section Caninae, and to examine the intraspecific differentiation within and among the European and Flemish populations. Our genetic results supported the subdivision of the European subgenus Rosa into several sections and the unique and peculiar position of the polymorphic section Caninae as was suggested by Henker. Within the section Caninae, a hierarchical structure was observed reflecting three morphologically well-distinguishable groups: Rubigineae, Vestitae, and Caninae. Although each group is characterised by consistent morphological characters, the genetical and morphological overlap between the groups is substantial and indicates the occurrence of interspecific hybridisation. Moreover, no arguments were found to support the subdivision of R. balsamica (subsection Tomentellae) from the subsection Caninae as was proposed by Henker. At the European scale, intraspecific geographical differentiation was observed within R. spinosissima, R. gallica, R. majalis, and R. pendulina. At the small geographical scale of Belgium, genetic differentiation was assessed within R. spinosissima. The Belgian R. arvensis populations displayed both genetic and morphological differentiation. In contrast, the observed genetic differentiation within the section Caninae tended to be related with the presence of several section Caninae taxa at a certain locality. The impact of (ancient) interspecific hybridisation events on the morphological and/or genetic variation of the section Caninae taxa is stressed. In the framework of conservation and use of autochthonous genetic resources, the observed intraspecific differentiation should be maintained if it is reflected in the genetic structure of the population and when it influences the ...