Because herbicide-resistant weeds have widely spread in the agricultural fields of grain-exporting countries, their seeds are introduced into grain-importing countries as contaminants in imported grain. Although Japan is a major importer of grain, few attempts have been made to investigate the establishment and expansion of such weeds that spilled from imported grain. So, we surveyed the distribution of herbicide-resistant individuals of Lolium species in Japan and compared their genetic variation with contaminant seeds in imported wheat by SSR polymorphism. Local populations were selected in 12 ports and two surrounding areas of Kashima port, Ibaraki Pref. and Sakaide port, Kagawa Pref. We detected herbicide-resistant individuals in ten out of 12 ports but not in the surrounding areas. The genetic structure analysis based on SSR detected two clusters. All port populations except one were assigned to the same cluster with contaminant seeds. The populations in a port where no grain is imported and the surrounding area of Kashima port were assigned to the other cluster. The populations in the surrounding area of Sakaide port mixed two clusters. This genetic heterogeneity seems to reflect whether the port is grain landing port or not and contaminant seeds may contribute to establishment of local populations in ports in Japan.