Abstract: 【Objective】In order to analyze the genetic diversity of the spotted scat(Scatophagus argus) in the northern South China Sea, clarify its population evolution history and distribution dynamics, and provide a scientific basis for the breeding, sustainable use of resources, and genetic diversity protection.【Method】The seven geographic S. argus populations collected in Dongshan, Fujian(DS), Yangjiang, Guangdong(YJ), Haikou, Hainan(HK), Weizhou Island, Beihai, Guangxi(BH), Qinzhou, Guangxi(QZ), Fangchenggang, Guangxi(FC), and Qinghua of Vietnam(TH) of the northern South China Sea were used as research objects. Based on the mitochondrial DNA cytochrome b gene(Cyt b) sequence analysis, DnaSP 5.10 was used to calculate the haplotype, haplotype diversity index(H_d), and genetic diversity index (π) of S. argus populations in the northern South China Sea. A phylogenetic tree of haplotypes was constructed by the neighbor joining method(NJ), a haplotype network diagram was constructed by the intermediary connection network method in Network 4.6, and the historical dynamics of S. argus populations was analyzed by the Tajima's D test, Fu's Fs test and nucleotide mismatch distribution methods.【Result】The 291 Cyt b gene sequences of the seven S. argus populations were defined as 33 haplotypes(Hap1-Hap33), among which haplotypes Hap1, Hap2 and Hap7 were stable dominant genotype formed during the long-term evolution of S. argus in the northern South China Sea.The H_d, π, genetic distance, genetic differentiation coefficient(F_st), and gene flow(Nm) of the seven geographic populations were 0.54103-0.77436, 0.00112-0.00171, 0.00113-0.00171,-0.01734-0.00364, 137.03888-inf, respectively. The haplotypes of different geographic populations were scattered irregularly on the haplotype phylogenetic tree, there was no systematic branch that clearly corresponded to a geographic population, and it did not show obvious geographic clustering distribution characteristics. The genetic variation among individuals within S. argus populations was 100.74%, indicating that all genetic variation came from individuals within populations, i.e., S. argus populations in the northern South China Sea had neither population differentiation nor group differentiation separated by Qiongzhou Strait. Both Tajima's D and Fu's Fs tests were significantly negative, and the nucleotide mismatch distribution was unimodal, indicating that S. argus populations in the northern South China Sea might have experienced an expansion event in history, which occurred about 34000 years ago, belonging to the late Pleistocene.【Conclusion】The genetic diversity of the seven geographic S. argus populations in the northern South China Sea belong to the diversity type of high haplotype diversity and low nucleotide diversity. The genetic distance between the populations is small, the genetic relationship is close, the genetic differentiation is not obvious, and there are frequent gene exchanges between populations and a high degree of genetic homogeneity, which is consistent with the hypothesis that S. argus in the northern South China Sea is a random mating population.