This study used microsatellite molecular markers and mitochondrial COI gene sequence information to investigate the effects of stock enhancement on Fenneropenaeus chinensis in the southern waters of the Shandong Peninsula, assessing the ecological contribution of the released F. chinensis. This species is an important economic shrimp species in China's Bohai and Yellow Sea regions, playing a key role in fishing and marine aquaculture. However, due to issues such as overfishing, disease, and environmental pollution, there has been a substantial decline in resources since the 1980s. To restore the dwindling resources of F. chinensis, China took the lead in conducting stock enhancement activities in the Bohai Sea. After nearly 40 years of continuous release, F. chinensis resources in the Bohai and Yellow Seas have been restored to some extent. The purpose of this study was to evaluate the effectiveness of stock enhancement of F. chinensis in the southern waters of the Shandong Peninsula using SSR (simple sequence repeats) and mitochondrial COI molecular marker technology. The experimental sample collection was divided into three stages. In the first stage, in May 2023, 404 parental F. chinensis were collected from Haiyang Yellow Sea Aquatic Products Co., Ltd. in the southern part of the Shandong Peninsula after the completion of production of released seedings. In the second stage, during the autumn fishing season of F. chinensis in September 2023, a total of 461 individual F. chinensis were recaptured in the sea areas of Huangdao, Haiyang, and Laoshan. In the third stage, from March to April 2024, 110 and 399 migrating individuals of P. chinensis were collected in the Laoshan and Rizhao sea areas, respectively. All the samples were frozen and transported to the laboratory for storage. Genomic DNA was extracted using the conventional phenol-chloroform isoamyl alcohol method, and DNA quality was detected by agarose gel electrophoresis and spectrophotometer. The experiment used parent–offspring tracing methods based on microsatellite molecular markers and mitochondrial COI gene sequence information to evaluate the effectiveness of stock enhancement of F. chinensis in the southern waters of the Shandong Peninsula. Eight polymorphism-rich microsatellite loci were used for PCR amplification and genotyping, combined with mitochondrial COI gene sequence analysis. Gene Mapper software was used to read allele data, and Cervus software was used for statistical analysis to determine potential parent-offspring pairs. The parentage relationship between released individuals and recaptured individuals was further verified using partial mtDNA sequence haplotypes. The results showed that 350 alleles were detected at eight SSR loci, with the number of alleles detected per locus ranging from 7 to 80, and the average number of alleles was 31.8. The observed heterozygosity (Ho) ranged from 0.606 to 0.896, the expected heterozygosity (He) ranged from 0.619 to 0.972, and the average polymorphism information content (PIC) value was 0.856. A total of five SNP polymorphic sites and seven haplotypes were detected in the COI sequence, with Hap01 accounting for 80% as the main type. The haplotype diversity was 0.065, and the nucleotide diversity value was 0.00033. A total of 121 individuals from stock enhancement were monitored in the recaptured samples from the autumn fishing season of 2023 and the migratory recapture samples of 2024. Further verification with mitochondrial COI gene sequences excluded nine unfit individuals. Among 970 recaptured individuals, 112 individuals from stock enhancement were detected, including 56 individuals from stock enhancement out of 461 individuals recaptured during the autumn fishing season of 2023, accounting for 12.4% of the total recaptured individuals. 56 individuals from stock enhancement were detected in the migratory recapture samples of 2024, accounting for 9.2% of the total recaptured individuals. Microsatellite markers showed high levels of genetic diversity, while mitochondrial DNA detected lower haplotype diversity. This is mainly because nuclear genes have higher levels of genetic variation. In the traceability analysis of stock-enhanced F. chinensis, SSR markers provided sufficient individual identification capabilities. However, the lower the number of bases in the repeat unit, the higher the level of simple sequence repeat variation. But dinucleotide repeats can produce rich variability while often causing deviations in allele reading results due to base mismatches and slippages during PCR, which affects the accuracy of parent–offspring tracing results. Therefore, it is necessary to combine it with mitochondrial COI gene sequences that strictly follow maternal inheritance for re-verification to ensure the accuracy of allele reading and correction. This study provides a detailed assessment of the effectiveness of stock enhancement of F. chinensis in the Yellow Sea located on the southern coast of the Shandong Peninsula. This indicates that the enhancement of F. chinensis in the southern waters of the Shandong Peninsula had a significant contribution to the biomass of autumn in the current year and the resources of reproductive migration in the following year. Evaluating the effectiveness of stock enhancement of F. chinensis in the Yellow Sea and the Bohai Sea is not only of considerable importance for the conservation of F. chinensis resources but also makes an important contribution to the local marine ecosystem. This study can provide a scientific reference for the stock enhancement of F. chinensis in the Yellow Sea and the Bohai Sea.