Abstract: This study was conducted to analyze the genetic diversity and genetic structure of wild Acanthopagrus latus populations in the southeastern coast of China by mitochondrial DNA control region including Ningde, Xiamen and Zhangpu in Fujian Province, Nan'ao Island and Zhanjiang in Guangdong Province, Haikou in Hainan Province and Beihai in Guangxi Zhuang Autonomous Region. Results showed that the mitochondrial DNA control region sequence of 48 individuals is 580 bp, and the haplotypes were 44. The haplotype diversity and nucleotide diversity of populations were 0.996 and 0.017 30, respectively. The level of genetic differentiation among seven A. latus populations was low, genetic distance between each population was 0.010 28-0.029 87. The F_ST between populations was from -0.068 41 to 0.545 86, and there was a certain level of genetic differentiation between Beihai population and other populations. AMOVA analysis showed that the genetic variation within the population was 83.34%, and most of the genetic variations occurred within the population. When Beihai population and other six populations were divided into two groups, AMOVA analysis showed that the proportion of genetic variations between two groups was 42.66%, and the level of genetic variations between two groups was relatively high. The phylogenetic tree showed that Beihai population clustered into one branch, and the other six groups clustered into another branch. The haplotype network based on TCS network showed that 44 haplotypes were mixed together, and there were no monophyletic groups among the populations. In summary, this study potentially provided theoretical basis for fishery management and germplasm conservation in the future.