Plants of the genus Berberis have been forbidden entry in Canada because common barberry (Berberis vulgaris) is an alternate host for black stem rust of wheat. Japanese barberry (Berberis thunbergii), an ornamental shrub appreciated for its hardiness and attractiveness, is generally considered immune to rust. Therefore, the Canadian government has established a program allowing importation of 11 approved Japanese barberry cultivars. The success of the program relies on the proper identification of the approved varieties, which may not always be possible when the plant is dormant or missing some essential morphologic criteria. Therefore, a cultivar verification method has been established using the amplified fragment length polymorphism (AFLP) genotyping technique. The method was validated using DNA extracted from 41 plants sampled across the country and representing 23 Japanese barberry cultivars and representative of the 11 approved cultivars. The method successfully differentiated and confirmed the identity of all approved cultivars. Furthermore, the method was able to detect and identify two of six samples submitted for cultivar verification as mislabeled by the exporter because the AFLP patterns generated did not correspond to their reference cultivar patterns.