The Rhinogobius species complex (Pisces: Gobiidae) includes great variation in colour, morphology and ecological form. In particular, R. sp. OR (Orange type) exhibits some of the greatest colour variation among the species complex, although the genetic relationships among the variations in this fish remain unclear. Thirteen microsatellite loci were identified from R. sp. OR, and all loci were polymorphic with two to 17 alleles per locus. Observed heterozygosity ranged from 0.1 to 0.9, while the expected heterozygosity ranged from 0.19 to 0.96. Multiplex polymerase chain reaction reaction (PCR) were optimized. All loci except Rhi-5 conform to Hardy–Weinberg equilibrium (P > 0.05).