Chromosome studies of Kirengeshoma palmata, a second-level endangered and rare species in China and Japan, have been creating misconceptions among researchers due to varying reports of 2n = 52 and 2n = 54 in relation to this species. Moreover, the karyotype of K. palmata has not been explained clearly thus far. Therefore, in this study, we aimed to confirm the exact number of chromosomes in K. koreana and K. palmata by securing this plant from Mt. Jirisan and Mt. Baekunsan on the Korean Peninsula and from Kochi and Miyazaki prefectures in Japan. In particular, enzyme digestion and scanning electron microscopy were utilized to determine most accurately the number of chromosomes for Kirengeshoma. Fluorescence in situ hybridization and flow cytometry were also undertaken to confirm the presence of polyploidy. The results of this study indicate that the controversial earlier finding of 2n = 52 chromosomes in Kirengeshoma is indeed accurate. The findings here also show that the total chromosome length ranges from 40.37 to 46.90 mu m in K. koreana and from 42.12 to 48.32 mu m in K. palmata. The average total chromosome length ranged from 43.52 +/- 2.37 in K. koreana and 45.07 +/- 2.58 mu m in K. palmata. However, secondary constrictions were not present in the two species of Kirengeshoma. In the fluorescence in situ hybridization study, 5S and 45S signals were detected in one pair each in K. koreana and K. palmata, and K. koreana according to flow cytometry results also showed diploid peaks. Therefore, the previously reported claim that K. palmata was auto-tetraploid is not supported. Rather, the results here confirm that the two species of Kirengeshoma are diploid, supporting earlier results from a recent study of population genetics. Our results also strongly support the contention that Kirengeshoma is closely related to the genus.