In this study, seven microsatellite markers were applied for analyzing polymophism of 492 samples collected from 12 wild and domesticated Asian seabass populations. The results showed significantly different between the wild and domesticated populations. The allele numbers in each locus varied from 11-21 alleles/locus in wild and from 3-8 alleles/locus in domesticated populations. Pairwise Fst did not perform significant differences among the wild groups from Hai Phong, Khanh Hoa, Vung Tau and Bac Lieu, however, there were significant differences among domesticated Asian seabass groups (Hai Phong, Khanh Hoa, Vung Tau, Ca Mau in comparison to Bac lieu, Kien Giang). The high genetic variation of wild Asian seabass populations will support to select genetic materials for better selective breeding programme.