Abstract: In order to analyze the genetic structure of Lateolabrax maculatus, we selected 11 polymorphic microsatellite loci from L. maculatus genome sequence to investigate the genetic structure of six wild populations of L. maculatus. All of the wild L. maculatus were fished from the coast of Tianjin, Qingdao, Changdao, Shanghai, Xiamen and Beihai, China, respectively. A total of 57 alleles were detected from 11 polymorphic microsatellite loci and 7 microsatellite loci were highly polymorphic loci. Among the six populations, the number of alleles (N_a) was 3.909 3–4.636 4 and the effective number of alleles (N_e) was 2.293 4–2.773 5. The observed heterozygosity (H_o) was 0.391 3–0.456 8 and the expected heterozygosity (H_e) was 0.505 1–0.566 2. The polymorphism information content (PIC) was 0.388 8–0.518 9. The populations of L. maculatus from Qingdao, Shanghai and Beihai had highly polymorphism, and the other populations had moderate polymorphism. The Shanghai population had the highest polymorphism among all the populations. Changdao and Xiamen populations had low polymorphism. The genetic differentiation index (F_ST) was 0.022 6–0.055 2. The genetic differentiation among the six population was low and the highest genetic differentiation was detected between Tianjin population and Beihai population. The gene flow (N_m) was 4.276 6–11.220 8, and the most frequent gene exchange was found among these populations. The analysis of molecular variance (AMOVA) shows that the variation among populations accounted for 91% and the variation within populations accounted for 9%. The cluster analysis based on individual classification shows that the individuals of six populations were divided into two genotype groups and no independent genotype group was detected. The UPMGA cluster tree based on genetic distance shows that six populations were divided into two branchs.