Rehmannia japonica is an endangered perennial herb species in Japan. Although six species of the genus Rehmannia are generally recognized, a seventh species, R. japonica, was described by Makino (1932). This species is considered to have been introduced from China and was widely cultivated as a horticultural plant in the 18th century in Japan. However, wild plants of this species are not known in China at present and have been reported from only two sites in Shizuoka Prefecture. In this study, we aimed to reveal the phylogenetic identity and the genetic diversity of R. japonica. The haplotype network based on the nucleotide substitutions and indels of two cpDNA regions (trnL-F and rps16) showed that the sequence of R. japonica was different from the other six species of Rehmannia, supporting the separate species status of R. japonica. The analysis of genetic diversity using 12 microsatellite loci showed that all 58 samples of R. japonica collected from two populations had an identical genotype while 15 individuals of the most related species, R. chingii, showed high polymorphism in 6 loci. This result suggests that microsatellite markers using here are useful for estimating the genetic diversity of R. japonica and this species survives as a single genet.