We identified Sagittaria plants distributed in Lake Yonuma (Iwate Prefecture, Japan) via DNA sequencing and also studied the morphology, distribution, and habitat at Lake Yonuma during 2012 and 2015. In addition, we cultivated plants in an outdoor aquarium. The internal transcribed spacer (ITS) region sequence of these unidentified Sagittaria plants completely matched that of S. natans Pall. from Hokkaido, Heilongjiang, Inner Mongolia, Sakhalin, and other GenBank data. In the field, almost all plants sprouted from vegetative propagules and tubers remaining on the parent plants. Some floating-leaved plants had stolons and new tubers. Although no plants flowered, under natural or cultivated conditions, genetic and morphological characteristics indicate that the plants were S. natans. The population in Lake Yonuma is a remnant population of S. natans in Japan and is located at the southeastern extent of the species distribution worldwide. This population of rare plants requires urgent protection.