Aldrovanda vesiculosa L. (Droseraceae), or waterwheel plant, is a threatened aquatic plant species, and it is quickly vanishing from the natural distribution range in the world. There used to be many localities of the species in Japan, but it was extinct from nature in the country in 1967. The information regarding the localities in Japan was recorded in various sources, but those had not been summarized yet. Therefore, the current study reviewed herbarium specimens and literature, and we documented each location of the species, the dates of discovery and extinction, and the cause of extinction. There were 35 locations, including four artificially introduced sites, in nine prefectures. It was hypothesized that the species had spread due to floods and had been established at each locality. We testified the hypothesis using a simulation map that the plants had spread by floods in the Kanto region, the major distribution area in the country. At the same time, serious floods destroyed some habitats of the species. However, human activities more seriously resulted in habitat loss. The species collected from the localities before the extinction has been under cultivation. Restoration of the habitat and reintroduction of the species has been attempted at a pond, but it is still on the way. The current study has summarized the causes of the extinction of A. vesiculosa in Japan, and it also aims to reduce the potential risk of extinction in extant populations of the species in the world as well as other threatened aquatic plants.