Dioecious shrubs, Lindera umbellata, L. praecox and L. obtusiloba produce seeds by mating between females and males. On the other hand, only females of L. glauca grow in Japan and they reproduce by apomixis. In this study, the genetic diversity and genetic structure were compared among the Lindera species with different breeding systems. From the Tohoku to Kyushu regions, the four Lindera species were sampled and single nucleotide polymorphisms (SNPs) were detected by MIG-seq. In the three sexual species, the proportions of number of loci with different genotypes among the common loci between a pair of parents were about 0.1-0.2. The values were about 0.05-0.1 between a parent and the seeds. The populations in the Kii Peninsula had a different allelic composition from other areas. In addition, in L. praecox, genetic differentiation was seen among populations in eastern and western Japan. In the L. glauca populations, the proportions of loci with different genotypes among the parents were 0.03-0.05. The values were 0.02-0.03 between a parent and the seeds. No genetic differentiation was observed among regions. Although the L. glauca population has extremely low genetic diversity, the demerit may be compensated by advantages of apomixis.