The Shu–Isewan region in central Honshu, Japan is an area in which unique wetland ecosystems have existed for millions of years. This ecological setting provides an excellent opportunity to examine how this palaeogeographical history has concomitantly affected the genetic variation of species now associated with one another. We examined this question by comparing the genetic structure and diversity of plant species characteristic of the wetlands. We collected leaves from individuals of nine species occurring in each of 68 wetlands. This was followed by the analysis of 468–1894 bp of non-coding plastid DNA. In addition, information on haplotype occurrences for two other species was obtained from previous studies. Based on the spatial patterns of plastid DNA variation, we performed a multivariate analysis. As a result, three geographical clusters were identified, reflecting the similarity of haplotype occurrences of the study species. In contrast, the locations in which rare haplotypes were concentrated differed markedly among species. The relatively high genetic diversity suggests that these plants have not experienced severe bottlenecks because wetlands provided adequately sized refugia. The plants are at risk of extinction by loss of wetlands, but remain an evolutionary legacy of an unusually stable geological history. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 78–94.