Interspecific hybrid families of female Haliotis diversicolor × male H. discus discus were produced and analyzed using amplified fragment length polymorphism (AFLP) technology to reveal the genetic makeup of F1 progenies. The survival rates of the hybrid F1 were very low, ranging from 0–0.13%. Twenty hybrid F1 from 3 families along with 3 different female parents and their common male parent were analyzed with 3 AFLP primer combinations. In total, 266 markers were detected. Genetic relationships among the progenies and the parents were evaluated by generating a similarity and genetic distance matrix. The genetic divergence between Haliotis diversicolor and Haliotis discus was at a high level, with genetic distance ranging from 1.471–1.492. The AFLP band patterns of hybrid F1 progeny were similar to those of the female parents, but were quite different from that of the male parent. The mean genetic distance between hybrid F1 and their female parents were 0.024–0.039, slightly less than that among the female parents, which indicates that the hybrid F1 shared high genetic similarity with their female parents, Haliotis diversicolor. However, 0–0.8% of total AFLP bands of each individual were found to be parental bands, and 0–3.3% were found to be nonparental bands. The possible reason for the presence of paternal-specific and nonparental bands is discussed.