Ranunculus nipponicus (Ranunculaceae) is a vulnerable aquatic macrophyte in the Kinki district, which is the southernmost distribution of this species in Japan. The present distribution and situation of the populations were assessed in the district in 2004. Comparison between the past distribution records and the present distribution revealed that six of the 15 past-reported localities had disappeared, whereas three localities were newly found in Shiga Prefecture. We confirmed 12 habitats of R. nipponicus in the Kinki district, of which seven habitats were distributed in Hyogo Prefecture and five habitats were found in Shiga Prefecture. Most of the extant populations have been found in concrete-lined canals or rivers, suggesting a vulnerable situation of their habitats. On the other hand, riverbeds of each habitats were covered with deposited mud, suggesting a possibility that the disappeared habitats of the plant could be restored with a seed bank germination.