Lathyrus japonicus commonly inhabits seashores. However it also grows near the shores of an inland lake (Lake Biwa, an ancient japanese freshwater lake) where it is assumed to have been isolated for a long time. The impact of this long-term isolation on phylogeographic and population structures is described. This reveals low genetic diversity due to the bottleneck effect. Implications for these dwindling inland populations and their conservation are discussed in this free—open access paper.