In this study, a total of 821 shrimps from four breeding population generations and a wild population of Fenneropenaeus chinensis (2015, 2016, 2017, and 2019) were sequenced using 2b-RAD technology to analyze the genetic diversity characteristics of artificial breeding and wild populations of F. chinensis, mining the selected single nucleotide polymorphism (SNP) sites in the continuous artificial selection process. A total of 83767 SNP sites were obtained by sequencing; F-statistics showed that the average coefficient of genetic differentiation (FST) between wild population and breeding populations was 0.022. The highest degree of genetic differentiation between the wild and breeding populations in 2019 was 0.0260; the lowest degree in 2015 was 0.0190. The FST between wild and breeding populations is less than 0.05, indicating weak genetic differentiation. The population principal component analysis results showed that the genetic structure between wild and breeding populations did not change significantly. The statistical results of genetic diversity showed that the average expected heterozygosity (He) of the wild population and the breeding populations were 0.1716 and 0.1806, respectively; the average observed heterozygosity (Ho) values were 0.1861 and 0.1943; and the average polymorphism information contents were 0.1428 and 0.1515. The mean values of nucleotide polymorphism (Pi) were 0.1732 and 0.1813. Among them, each genetic diversity index of the selected populations in 2017 and 2019 was significantly different compared to the wild population (P＜0.05). Selection and elimination analysis of different generations of breeding and wild populations yielded 92, 103, 166, and 117 selected SNP loci; the number of common loci was 4. The number of common sites with allele frequencies increasing generation by generation between adjacent generations of selective breeding populations was 7107, of which 3674 sites deviated significantly from the Hardy-Weinberg balance (P＜0.05). The allele frequency between adjacent generations of breeding populations decreased to 8501, of which 4101 loci significantly deviated from the Hardy-Weinberg equilibrium (P＜0.05). Results indicate that the population genetic diversity and genetic structure of F. chinensis have not changed significantly after artificial selection and breeding, and a high genetic selection potential is maintained.