Genetically modified (GM) Brassica napus derived from spilled seeds have been found over the years along roads around the oilseed import ports in Japan. Large populations of B. juncea, a relative species of B. napus, are often observed along riversides in Japan. If gene flow occurs from GM B. napus to wild B. juncea, and if the transgene enhances its fitness, this hybrid with improved fitness traits can raise concerns about it possibly becoming invasive and displacing native vegetation. Although seed production is essential to evaluate fitness, the availability of information regarding such ecological knowledge as the seed production of wild B. juncea is limited. Therefore, we conducted quantitative research on B. juncea seed production at six natural habitats along riversides in Japan to obtain baseline yield data for assessing the risk of GM B. napus. The seed production of B. juncea varied largely among individual plants within and across habitats. The average total seed production number was 3,800 per plant, which was two to eight times greater than that of neighboring B. rapa.