Genetic diversity and phylogenetic relationships of four morphologically similar and sympatric grouper species,namely Yellow grouper(Epinephelus awoara),Hongkong grouper(E.akaara),Duskytail grouper(E.bleekeri) and Honeycomb grouper(E.merra) were investigated.Specimens were sampled from sea area of southern China.Calculation based on genotypes of nine microsatellite DNA loci showed that the genetic diversity of the four grouper species was high with the mean number of alleles,average polymorphic informative content(PIC),average observed heterozygosity(Ho) and average expected heterozygosity(He) being from 8.22 ± 5.02 to 18.67 ± 9.38,from 0.56 ± 0.21 to 0.83 ± 0.13,from 0.62 ± 0.03 to 0.85 ± 0.02,and from 0.60 ±0.07 to 0.86 ± 0.04,respectively.Tests of Hardy-Weinberg equilibrium(HWE) demonstrated that,except for those of Duskytail grouper,most loci of the rest three grouper species were under equilibrium conditions.Phylogenetic trees reconstructed from both genotypes of microsatellite DNA loci and partial mitochondrial cytochrome b gene(mtDNA Cyt b) sequences indicated that Yellow grouper and Hongkong grouper were more closely related among the four species.Furthermore,Bayesian cluster on the genotypes of nine microsatellite DNA loci for all individuals of the four grouper species supported their genetic distinctiveness.