Acanthopagrus latus is a valuable marine fish and an important economic fish for marine aquaculture along the South China coast. In order to ascertain the genetic diversity and genetic differentiation status of A. latus populations distributed along the South China coast, in this study, the mitochondrial control region (D-loop) gene sequences were used to analyze the genetic diversity and population genetic structure of eight A. latus populations from the South China coast, including Xiamen, Shanwei, Yangjiang, Haikou, Sanya, and Beihai, Qinzhou, Qinzhou and Fangcheng. The results showed that 320 D-loop sequences from the eight A. latus populations were 947-958 bp in length. Totally, 29 insertion or deletion sites and 210 mutation sites (including 142 parsimony information sites and 68 single mutation sites) were detected in the D-loop sequences; overall mutation sites, haplotype number, and haplotype diversity (H_d), average nucleotide difference and nucleotide diversity (π) were 210, 268, 0.998 43, 14.790 65 and 0.01570, respectively. The results of cluster analysis showed that all populations were clustered into two groups, east and west separated by Qiongzhou Strait. The genetic differentiation coefficient (F_ST) between the eight populations was –0.01268-0.466 74, and gene flow (N_m) was 0.571 26~∞. The variance analysis showed that the genetic variation between groups, between populations within groups, and between individuals within populations were 33.42%, 0.32%, and 66.26%, respectively. Neutral tests showed that Tajima's D was –1.694 77 (P=0.010 00) and Fu 's Fs was –23.683 39 (P=0.00600), indicating that A. latus along the South China coast experienced a population expansion event. This study indicated that the genetic diversity of A. latus populations along the South China coast was relatively rich. This study suggested that A. latus populations can be divided into two management units by the Qiongzhou Strait, the east group and the west group for germplasm protection. Based on such monitoring results, some countermeasures and suggestions for the future restoration strategy were proposed so as to provide a theoretical basis for restoring and protecting the A. latus populations, and meanwhile it can also provide some scientific guidance for artificial breeding and value-added release in natural sea area.