Premise of the study: Polymorphic microsatellite primers were developed in the seagrass Zostera japonica to investigate genetic variation and to identify clonal structure. •
Methods and results: Thirteen polymorphic loci and 23 monomorphic loci were developed in Z. japonica. Two to 13 alleles per locus were observed at the polymorphic loci across 57 individuals of two Z. japonica populations. The observed and expected heterozygosities within populations ranged from 0.0000 to 1.0000 and from 0.0000 to 0.8542, respectively. •
Conclusions: Our study showed high-level polymorphism at the polymorphic loci in Z. japonica. These primers would be a powerful tool to study genetic variation, clonal structure, and mating systems.