Lanceleaved waterplantain is an exotic weed of rice that was introduced into Australia in the 1930s. Since its introduction, it has spread throughout much of the rice-growing region in southeastern Australia. The variability of lanceleaved waterplantain in these regions was studied using polymerase chain reaction-based, inter simple sequence repeat (ISSR) analysis. Deoxyribonucleic acid fingerprints from samples of the weed from southeastern Australia were compared between locations and with two samples of common waterplantain, a closely related species. The analysis indicated that there were two distinct groups of lanceleaved waterplantain that correlated with location. From the results of multidimensional scaling analysis, it is hypothesized that the Griffith group did not arise from hybridization between lanceleaved waterplantain and common waterplantain, and that it is more likely that the group arose from a separate introduction into the area. It is also suggested that there is seed movement between areas in the Murray Valley and Colleambally Irrigation areas. The implications of this variation for biological control of the weed are discussed.