To reveal the effects of herbicide selection on genetic diversity in the outcrossing weed species Schoenoplectus juncoides, six sulfonylurea-resistant (SU-R) and eight sulfonylurea-susceptible (SU-S) populations were analysed using 40 polymorphic inter-simple sequence repeat loci. The plants were collected from three widely separated regions: the Tohoku, Kanto and Kyushu districts of Japan. Genetic diversity values (Nei's gene diversity, h) within each SU-S population ranged from h = 0.125 to h = 0.235. The average genetic diversity within the SU-S populations was H-S = 0.161, and the total genetic diversity was H-T = 0.271. Although the HS of the SU-R populations (0.051) was lower than that of the SU-S populations, the H-T of the SU-R populations (0.202) was comparable with that of the SU-S populations. Most of the genetic variation was found within the region for both the SU-S and SU-R populations (88% of the genetic variation respectively). Two of the SU-R populations showed relatively high genetic diversity (h = 0.117 and 0.161), which were comparable with those of the SU-S populations. In contrast, the genetic diversity within four SU-R populations was much lower (from h = 0 to 0.018) than in the SU-S populations. The results suggest that selection by sulfonylurea herbicides has decreased genetic diversity within some SU-R populations of S. juncoides. The different level of genetic diversity in the SU-R populations is most likely due to different levels of inbreeding in the populations.