Genetic variability of greater amberjack used as seed fish in aquaculture was examined, and compared with those of collected from coast waters of Japan and artificial propagated activity. The genetic variability was assessed using polymorphism of microsatellite DNA (MS) and the mitochondrial DNA (mtDNA) D-loop markers. The average alleles number per locus were 11.0, 11.5 and 4.3 for aquaculture, natural and artificial seed respectively, while the average observed (and expected) heterozygosities were 0.701 (0.778), 0.654 (0.738) and 0.532 (0.540). Thirty-three mtDNA haplotypes were detected following digestion of D-loop sequences with five endonucleases: Taq I, Hae III, Mbo I, Rsa I and Hinf I. Significant genetic difference was observed among seed population of greater amberjack. Nei's genetic distances based on the two loci MS revealed at least two genetically different sub-populations of greater amberjack were used in the aquaculture farm Japan.