Synechogobius hasta is an important commercial marine fish with distinctive features of rapid growth and short lifespan. We isolated and characterized 17 microsatellite markers for S. hasta using a (GT)(13)-enriched genomic library. Polymorphism was assessed in 48 individuals from a single population collected from the northern coastal waters of the Yellow Sea. The number of alleles per locus ranged from 2 to 23, with a mean of 11.3. The observed and expected heterozygosities ranged from 0.130 to 1.000 and from 0.123 to 0.939, with means of 0.758 and 0.774, respectively. Fourteen of 17 loci conformed to Hardy-Weinberg equilibrium and no significant linkage disequilibrium between locus pairs was detected. These microsatellite markers will be useful for population genetic structure analyses.