We developed 18 novel microsatellite markers for Onychodactylus japonicus using Illumina Miseq System, and tried cross-amplifications in three congeners. The number of alleles and expected heterozygosity at each locus in O. japonicus were 3–15 (mean=6.83) and 0.45–0.89 (mean=0.73), respectively. Cross-amplifications in congeners succeeded in 9–13 of 18 loci, and eight loci were consistently amplified across all four species. The markers described here will be useful not only for investigating phylogeography and fine-scale genetic structure, but also for estimating genetic diversity of endangered species or populations for conservation management.