We isolated and characterized 11 microsatellite markers for Ovophis okinavensis, a viperid species endemic to the Ryukyu Archipelago. These markers showed polymorphism among 25 individuals from Okinawajima Island. The number of alleles per locus was 3–11, and observed and expected heterozygosity were 0.240–0.960 and 0.218–0.853, respectively. Cross-amplification confirmed that at least seven out of the 11 microsatellite markers were applicable to a putative relative, Trimeresurus gracilis. The markers provided here are expected to be valuable for population- and/or individual-level genetic studies of not only O. okinavenesis, but also its relatives.