Amplified fragment length polymorphism (AFLP) analysis of the population genetic structure and genetic diversity of Haliotis discus hannai (D), Haliotis gigantea (G), and their reciprocal hybrids D ♀ × G ♂ (DG) and G ♀ × D ♂ (GD) was carried out in this study. A total of 479 unambiguous and highly repeatable AFLP markers, 311 of which (64.93%) were polymorphic, were obtained using 7 primer combinations. The reciprocal hybrids inherited bands from both parents, indicating that the hybrids were truly heterogeneous. The Shannon diversity index for D, G, and their reciprocal hybrid populations DG and GD was 0.169 ± 0.188, 0.211 ± 0.227, 0.236 ± 0.267, and 0.231 ± 0.242, respectively. Analysis of molecular variance revealed that 29.58% of the variance was among populations, whereas 71.42% of variance was within populations. Genetic distance was maximum (0.681) between D and G, and was minimum (0.482) between GD and G. The 4 populations were clustered into 2 major clades using the unweighted pair group method with arithmetic mean. All genetic parameters indicated that there was plentiful genetic diversity in the reciprocal hybrids of D × G. Results of this study suggest that these AFLP markers can be used in the future to enhance current breeding practices in abalone culture because of the large numbers of polymorphic markers.