Objective The purpose of this study is to systematically analyze the genetic diversity, population genetic structure and differentiation characteristics of abalone cultured populations, thereby providing a scientific basis for genetic selection and germplasm resource conservation in abalone.

Methods Using SSR technology, we analyzed genetic diversity in the four abalone cultured populations in Fujian Province including Haliotis discus hannai (ZPB), Haliotis discus hannai ♀ × H. fulgens ♂ (LPB), ZPB ♀ × LPB ♂ (LZB) and Haliotis discus hannai ♀ × H. gigantea ♂ (XPB).

Results The results showed the average number of alleles (N_a) was 16 across seven loci, with the effective number of alleles (N_e) ranging from 2.856 to 11.517. Observed heterozygosity (H_o) ranged from 0.410 to 0.930, while expected heterozygosity (H_e) was between 0.653 and 0.918, with polymorphism information content (PIC) spanning 0.611 to 0.907. The genetic distance between LZB and XPB was the smallest (0.106), and the identity (I) was the highest. The genetic distance between LPB and XPB was the largest (0.440), and the identity was the lowest. The degree of fixation statistics (F_st) among populations ranged from 0.000 to 0.069, and the number of migrants (N_m) ranged from 3.378 to 999.750. Analysis of molecular variance (AMOVA) revealed that 4% of genetic variation originated from among populations, 10% from among indiviual, and 86% from within indiviual. Four cultured abalone groups could be divided into three groups.

Conclusion The genetic diversity of LPB and ZPB populations is low, and the genetic diversity of LZB and XPB populations is high. These resluts provide evidence for the change trend of genetic diversity of abalone culture population, and provide reference for the scientific management of abalone resources and the healthy development of aquaculture industry.