Research Highlights: genetic diversity in populations were compared among related shrub species with different reproductive systems. Background and Objectives: Lindera species are dioecious trees or shrubs that produce seeds by mating of males and females. To evaluate the importance of genetic diversity for the persistence of natural populations, we compared genetic information among four Lindera species in Japan. Three are dioecious shrubs (Lindera praecox, Lindera umbellata, and Lindera obtusiloba) that produce seeds by sexual reproduction. The remaining species, Lindera glauca, reproduces by apomixis; only female plants are found in Japan. Materials and Methods: all four species were sampled across a wide geographic area, from Tohoku to Kyushu, Japan. Single nucleotide polymorphisms (SNPs) were detected by multiplexed ISSR genotyping by sequencing (MIG-seq) and the resulting genetic diversity parameters were compared among populations. Results: in all sexually reproducing species, the values of observed heterozygosity were close to the expected ones and the inbreeding coefficients were nearly 0. These results were supposed to be caused by their obligate outcrossing. The genetic difference increased, in ascending order, between a mother plant and its seeds, within populations, and across geographic space. We observed a substantial geographic component in the genetic structure of these species. For L. glauca, the genetic difference between a mother and its seeds, within populations, and across space were not significantly different from what would be expected from PCR errors. Genetic diversity within and among populations of L. glauca was extremely low. Conclusions: apomixis has the advantage of being able to found populations from a single individual, without mating, which may outweigh the disadvantages associated with the extremely low genetic diversity of L. glauca. This may explain why this species is so widely distributed in Japan. Provided that the current genotypes remain suited to environmental conditions, L. glauca may not be constrained by its limited genetic diversity.