Abstract: In order to explore the impact of cross-regional introduction on the genetic diversity of Mytilus coruscus populations and the degree of genetic differentiation between regions, thereby providing a scientific basis for the protection of its germplasm resources, the samples of Mytilus coruscus were collected from the reefs of Pingtan (Fujian) and Zhoushan Islands (Zhejiang). Then, the genetic evolution analysis was conducted by using the mitochondrial COI gene and nuclear H3 gene. The results showed that there was no difference in the H3 gene of Mytilus coruscus between the two populations from Pingtan (Fujian) and Zhoushan (Zhejiang), so it was not suitable for the study of genetic structure. The COI gene sequences of Mytilus coruscus from the two populations were 661 bp in length, with an A+T content of 60.0%. They exhibited the genetic variations suitable for analysis, conform to the characteristics of mitochondrial molecular markers, and the sequences were stable and reliable. Therefore, the COI gene was chosen for the subsequent analysis of the population genetic diversity of Mytilus coruscus. A total of 32 polymorphic sites and 19 haplotypes were detected in the COI gene sequences of the two Mytilus coruscus populations. The overall haplotype diversity (H_d) was 0.9373, and the nucleotide diversity (P_i) was 0.00682. Among them, the genetic diversity of the Pingtan (Fujian) population (H_d=0.9579, P_i=0.00848) was higher than that of the Zhoushan (Zhejiang) population (H_d=0.8421, P_i=0.00404). The genetic differentiation coefficient (F_st) between the two Mytilus coruscus populations was 0.00196 (P＜0.01). The AMOVA analysis showed that 92.07% of the genetic variation in the two Mytilus coruscus populations came from within the populations. The haplotype network and UPGMA tree of the two Mytilus coruscus populations showed that only 2 of the 19 haplotypes were shared, and there was an obvious geographical branching structure. The results provided a basis for the protection and sustainable utilization of Mytilus coruscus germplasm resources.