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The Giant grouper (Epinephelus lanceolatus) is a coral fish with high commercial value in Southeast Asia.To investigate the genetic population structure for conservation, we isolated and characterized 20 microsatellite loci from from a CA enriched genomic library of Giant grouper.The number of observed alleles ranged from 3 to 15 and The observed and expected heterozygosities of all 20 polymorphic loci ranged from 0.036 to 0.821 and from 0.179 to 0.964 respectively.Seven loci significantly deviated from Hardy-Weinberg equilibrium.These microsatellite markers will provide helpful tools for develop of genomic databases and population genetic analyses of Giant grouper.