We evaluated the actual distribution, present status, and number of remnant individuals of Korean Sagittaria aginashi (Alismataceae) based on herbarium specimens and field surveys. We also reidentified Korean S. aginashi by analyzing sequences of the internal transcribed spacer (ITS) region. We found nine specimens of S. aginashi in herbaria from four localities housed at the Osaka Museum of Natural History (OSA) and at the Korea National Herbarium (KH). During our field research, we could not confirm the current statuses of two collection localities (Taereung and Ansan-si), though this was not the case for Ulsan-si. In addition, we found two new localities in Ulsan-si and Yangsan-si. These three remnant populations are distributed in wetlands in mountainous areas (elev. 480–740 m). With regard to the number of flowering and immature individuals in the three localities, there were <50 and <2,000, respectively, in total. ITS sequences demonstrated that the sequences of Korean and Japanese S. aginashi are uniform and distinct from other Sagittaria species. These results indicate that S. aginashi is a rare and threatened species in Korea. It should be listed as an endangered species on the Korean Red List and requires urgent protection by conservation programs, including the extensive surveys of other possible natural habitats.