Abstract: Atrina pectinata is a commercially important species in the Northern South China Sea. This study analzyed genetic diversity and genetic structure of A. pectinata in Northern South China Sea based on 191 individuals of 7 populations using Cytochrome Oxidase Ⅰ(COⅠ) sequence. A 600bp segment of COⅠ genes were sequenced, from which 113 polymorphic sites were tested and 73 haplotypes were defined. The total population in Northern South China Sea had high haplotype diversity (0.8996) and high nucleotide diversity (0.0257). However, 6 populations in L1 group (ST, YJ, ZJ, HK, QH, BH) had high haplotype diversity (0.8133—0.9286) and low nucleotide diversity (0.0033—0.0045). Based on neighbor-joining tree and haplotype network, 7 populations were classified into two groups, named L1 group and L2 group (FCG), and no clustering corresponding to sampling localities was found in L1 group haplotypes. F_st analysis showed no obvious genetic differentiation among 6 populations in L1 group (F_st= –0.0200— –0.0055, P>0.05) and significant genetic differentiation between L1 group and L2 group (F_st=0.8729—0.8821, P<0.01). Both Tajima’s D (D= –2.3190, P=0) and Fu’s F_s (F_s= –26.7990, P=0) of L1 group yielded significant negative values. Unimodal distribution was observed in L1 group. However, in L2 group, Tajima’s D (D= –1.4320, P=0.0565) was insignificant negative value, and Fu’s F_s (F_s=4.9540, P=0.9620) was insignificant positive value. These data implied L1 group and L2 group might have differentiated into two populations. The frequent gene exchange resulted in high genetic homogeneity among 6 populations in L1 group.