Stock enhancement is a fishery management approach involving the release of hatchery organisms to increase the abundance of natural fish or invertebrate population. In this study, genetic evaluation of Fenneropenaeus chinensis stock enhancement was carried out based on the mitochondrial DNA control region. The haplotype diversity (H_d) and nucleotide diversity (π) of broodstock populations were generally higher than that of recaptured populations. The molecular variance analysis (AMOVA) results demonstrated that genetic variance was in connection with the time of releasing and recapture. A significant pairwise F_ST value was only obtained between L1CY and C2LZ. But there was no obvious correlation between their geographical distance and genetic difference, confirming that time factor might be the leading cause of differences. Haplotypes shared by more than three individuals all could be recaptured, which indicated that the enhancement experiment was relatively successful. In general, the enhancement effect in 2012 was better than that of in 2013.