An important part of the assessment of the potential environmental impact from the introduction of a genetically modified (GM) plant is an evaluation of the potential for gene flow from the GM plant to related wild species. This information is needed as part of the risk-assessment process, in the context of whether gene flow to wild species is possible. One method for evaluating gene flow is to use molecular techniques to identify genes in wild species populations that may have originated from a cultivated species. An advantage of this method is that a phenotypic marker or trait is not required to measure gene flow. In the present study we analyzed the seedlings of seeds from three wild native Rosa species (R. multiflora Thunb., R. luciae Rochebr. et Franch. ex Crép. and R. rugosa Thunb.) selected from several locations across Japan where the wild rose was growing in close proximity to cultivated rose plants (Rosa×hybrida). To determine whether gene flow from cultivated rose had occurred, young leaves of 1,296 seedlings from the wild Rosa plants were analyzed by PCR for the presence of the KSN locus. This locus originated from a sport of R. chinensis Jacq. var. spontanea (Rehd. et Wils.) Yu et Ku and is involved in the recurrent flowering phenotype observed for cultivated rose hybrids, but is absent in Japanese species roses. The KSN locus was absent in all seedlings sampled, indicating no gene flow to wild Rosa species from the cultivated rose had occurred, and providing evidence that the probability of gene flow from cultivated to wild Rosa species in Japan is low or non-existent.