This experiment was to study the genetic structure of E.awoara,which could realize effective resource conservation and sustainable use of this species.PCR was used to amplify the complete sequences of the mitochondrial DNA(mtDNA)D-loop region of 53 individuals of E.awoara collected from Dongshan Bay.Because 5' end contained different numbers of repeat sequence units(RSU)and D-loop region had base insertion or deletion,sequences length of 53 E.awoara individuals ranged from 956 bp to 1 230 bp.53 E.awoara individuals were divided into three groups:2RSU(11.3%),3RSU(77.4%),4RSU(11.3%).Sequences were analyzed with the MEGA(version 3.0)and DnaSP(version 4.0)softwares.The results showed as follows:The average content of T,C,A and G was 33.4%,17.3%,35.4% and 13.9%,respectively.179 polymorphic sites were detected yielding 53 haplotypes.The average genetic distance of haplotypes is 0.019 7.The haplotype diversity was 1.000(H_d).The nucleotide diversity was 0.017 2(π).It is concluded that the genetic diversity of the E.awoara population in Dongshan Bay was at a medium level in mitochondrial DNA control region sequences.