In this paper, genetic diversity of intraspecies, and genetic relationship of interspecies in Epinephelus spp. (E. merra, E. fario, E. awoara, E. akaara and E. septemfasciatus) were assessed by using mitochondrial DNA restriction fragment length polymorphisms (mtDNA RFLPs).The samples were collected from the coastal area of Zhanjiang,Guangdong province. MtDNA was extracted from the fresh liver tissue by applying a difference centrifugation procedures. Using 17 restriction enzymes with 5-or 6-bp recognition sites, the purified mtDNA was cleaved by single enzymes. These enzymes included BamH Ⅰ，Bgl Ⅰ，Bgl Ⅱ，Dra Ⅰ，EcoR Ⅰ，EcoR Ⅴ，Hind Ⅲ，Kpn Ⅰ，Mlu Ⅰ，Pst Ⅰ，Pvu Ⅱ，Sal Ⅰ，Sca Ⅰ，Sma Ⅰ，Sty Ⅰ，Xba Ⅰ and Xho Ⅰ. The phylogenetic analysis was done using the Neighbor joining(NJ) method and Unweighted pairgroup method with arithmetic mean(UPGMA) method. Genetic diversity indices such as haplotype diversity (h), average genetic distance between haplotypes (P) and nucleotide diversity (π) were calculated using Nei and Li's segment method to quantify the genetic diversity within species. There were 8, 5, 8, 5 and 2 haplotypes detected within E. merra, E. fario, E.awoara, E.akaara and E. septemfasciatus, respectively. The haplotype diversity (h) was 0.8943, 0.6186, 0.9242, 0.6927 and 0.1820,respectively. The average genetic distance between haplotypes (P) was 0.62%±0.31%, 0.64%±0.37%, 1.12%±0.55%,0.72%±0.42% and 0.45%, respectively. And the nucleotide diversity (π) was 0.22%, 0.13%, 0.46%, 0.17% and 0.04%, respectively. The wild groupers in the Zhanjiang Coastal Area exhibited a relative higher level of genetic diversity. The net genetic distance between species (P_net) was 0.0694（E. merra - E. fario）,0.1337（E. merra - E. awoara）,0.1090 E. merra -E. akaara）, 0.1286（E. merra - E. septemfasciatus）,0.1590（E. fario -E. awoara）,0.0825（E. fario -E. akaara）,0.1153（E. fario - E. septemfasciatus）,0.1131 E. awoara - E. akaara）,0.0724（E. awoara -E. septemfasciatus） and 0.1336（E. akaara - E. septemfasciatus）. Both NJ and UPGMA methods yielded an identical phylogenetic tree for the five species. The E. merra and E. fario first clustered together, then joined with E. akaara, and finally clustered with E. awoara and E. septemfasciatus.