The subgenus Rosa is very intriguing but complex. Nowadays, many European taxonomists apply the taxonomical structure of Henker (2000), although other classifications and views are still considered. In order to gain insight in the taxonomical structure, 1,144 individuals belonging to 27 different wild rose species and some spontaneous hybrids were sampled in Belgium, France, Germany, The Netherlands and Scandinavian countries. Using AFLP analysis, the intra- and interspecific genetic variation was evaluated. PCO analysis supported the major subdivision of the subgenus Rosa in different sections and subsections according to Henker (2000). However, the position of R. tomentella in a separate subsection or within the subsection Caninae is questioned. In order to support the preservation and use of autochthonous genetic resources the genetic fingerprints of several populations were compared. It is concluded that wild populations of rare or locally prevailing species, accessioned from different regions, show genetic differentiation. However, for the common and well-dispersed species no differentiation was found.