Fourteen polymorphic microsatellite loci were isolated from the Japanese smelt (Hypomesus nipponensis). These microsatellite markers were tested in a sample of 24 individuals. The number of alleles ranged from 3 to 25, with an average of 8.4 alleles per locus. The observed and expected heterozygosity of these loci varied from 0.266 7 to 1.000 0 and 0.282 5 to 0.932 2, respectively. Locus HN 075 and HN 250 deviated significantly from Hardy Weinberg equilibrium (P<0.05). No genotypic disequilibrium among loci was found (P<0.05). These microsatellite markers could be useful in studing population structure of the Japanese smelt, or introduction routes of this fish to China.