Pacific abalone Haliotis discus hannai is one of the most important species of shellfish aquaculture. The annual production of cultured abalone exceeded 100,000 t in 2013, and the Pacific abalone was the main farmed species. The genetic diversity of hatchery stocks of H. discus hannai in most areas of China, however, remains unknown. The exchange of Pacific abalone in China was not only among hatcheries but also between southern and northern areas, and the Japanese population was widely used for the production of seed. Both practices may have led to the production of mixed seeds, and the difference between populations may be not significant, which could result in inbreeding and loss of potentially valuable alleles. Therefore, it is necessary to assess the current genetic characterization of hatchery populations. For the analysis, a total of 10 populations were obtained from different hatcheries: Dalian, Qingdao, and Changdao in the northern coastal areas; and Xiapu, Lianjiang, Putian, Zhangpu, Jinjiang, Dongshan, and Shanwei in the southern coastal areas. Five populations were added as the control: Ja (the F1 population of H. discus hannai introduced from Japan), KDH (the F1 population of H. discus hannai introduced from Korea), KDD (the F1 population of Haliotis discus discus introduced from Korea), ST (the F1 population developed from the cross of H. discus discus and H. discus hannai), and Red (the Pacific abalone with red shell). The data of 14 microsatellite primers were all highly polymorphic while the degree of variability was different at each locus. In all the studied populations, the number of alleles ranged from 2 to 17, and the number of effective alleles ranged from 1.032 to 10.169. The principal component analysis result showed that all populations were dispersed except KDD and ST, which clustered in the second and third quadrants. A neighborjoining tree indicated that most populations were closely related. Moreover KDH, KDD, and ST were less related to the others because of the different genetic background. The estimates of effective population size (N_e) using the linkage disequilibrium methods demonstrated that the N_e of eight populations was less than 50, and the other two populations were close to 50. In conclusion, by the previous studies, the current analyses present that these cultured populations of Pacific abalone in China have lost their genetic diversity to some extent, and the difference among populations was not significant. Thus, for the sustainable development of the aquaculture, the genetic diversity should be monitored every year and inbreeding should be controlled.