Pacific abalone (Haliotis discus hannai) is an important marine shellfish in China, which is naturally distributed in the coastal areas of Shandong Peninsula and Liaodong Peninsula, and has high economic and nutritional value. Since the 1990s, with the extensive application of hybridization technology, the cultivation industry of H. discus hannai has gradually moved from northern to southern China and developed rapidly. In 2019, the production of H. discus hannai and its hybrid offsprings in China has reached 180 000 tons. However, the process of artificial breeding and selection may reduce the genetic diversity index of species, change the genetic structure, or even cause genetic differentiation of populations. In order to explore the possible effects of cultivation patterns on the genetic structure of Pacific abalone in China in the last 30 years, 259 individuals were collected from Dalian (DL), Rongcheng (RC), Zhangzhou (ZZ), Tuoji Island (TJ), Daqin Island (DQ), and Nanhuangcheng Island (NH), the last three island belonging to the Changshan Archipelago of China. The mitochondrial cytochrome C oxidase subunit (COⅠ) gene and cytochrome B (Cytb) gene sequences were amplified by polymerase chain reaction (PCR) and sequenced on an automatic sequencer by using forward and reverse primers. Bioedit 7.0.5, DNAsp 5.10, MEGA 6.06 and Arlequin 3.5 software were used for sequence analysis. After sequence matching and shearing, 730 bp fragment length of COⅠ and Cytb genes were obtained. The results showed that 48 mutation sites and 30 haplotypes were detected in the 730 bp COⅠ sequence of 259 individuals; the haplotype diversity of the 6 populations ranged from 0.586 to 0.897, and the nucleotide diversity was 0.0056-0.0081; 59 mutation sites and 32 haplotypes were detected in the 730 bp Cytb sequence of 259 individuals. The haplotype diversity ranged from 0.605 to 0.909 and the nucleotide diversity was 0.0077-0.0120 in the 6 populations. The results of F_st and AMOVA among populations based on COⅠ and Cytb genes showed that there was significant genetic differentiation between most populations, and the genetic variation mainly existed between individuals but within populations. The current cultivation mode of H. discus hannai enhanced the gene exchange between different populations, and the secondary contact of populations with different genetic backgrounds resulted in high haplotype diversity and nucleotide diversity in all 6 populations. Different breeding standards in different breeding populations may be an important reason for the significant genetic differentiation. The evaluation of genetic resources of six Haliotis discus hannai populations in the northern and southern China coasts conducted in this paper provides a scientific basis for the rational utilization of the resources in China and the influence of breeding modes on genetic structure.