Eighteen polymorphic microsatellite loci from the giant mottled eel (Anguilla marmorata) were identified and their characteristics were described. These markers were tested in two wild populations from China (n = 20) and Australia (n = 20) respectively. The number of alleles ranged from 9 to 14 with an average of 11.28 per locus. The mean expected heterozygosity (H(E) ) was 0.8696 in the population from China, 0.8823 in the population from Australia. No locus deviates significantly from Hardy-Weinberg proportions (P < 0.05).