In Japanese Chionographis, populations are either hermaphroditic or gynodioecious, and diploid or tetraploid. The average level of inbreeding was compared among these populations by estimating Wright's fixation index. The estimates were significant in all gynodioecious populations irrespective of ploidy level, and hermaphrodites in gynodioecious populations are considered to be selfing. In hermaphroditic populations, f values were not significant in diploid taxa but were significant in tetraploid taxa. These results suggest that gynodioecy evolved only in selfing populations and support a traditional view that the outcrossing advantage of females plays an important role in the evolution of gynodioecy. Estimates of various genetic diversity measures suggest that tetraploid hermaphroditic populations experienced population bottlenecks, and females may have been lost historically.