Six novel microsatellite loci, containing (GA)(15\N17) or (GT)(10\N19) perfect tandem repeats, were isolated and characterized for the catadromous eel Anguilla japonica. The allelic size of the 6 loci ranged from 79 to 226 bp in length. All loci were polymorphic with a mean number of 14.7 alleles per locus and a mean heterozygosity of 0.67, suggesting higher polymorphism than that of freshwater and anadromous fishes, but lower than that of marine fishes. Genotype diversity of the 6 loci ranged from 0.22 to 0.61 with a mean value of approximately 0.5. Cross-species amplification showed that 5 of the 6 microsatellite primers proved to be useful in addressing questions of population genetics for all Anguilla species.