To determine the genomic composition of the interspecific hybrid between Haliotis diversicolor supertexta ♀ and H. discus discus ♂ at an early developmental stage, veliger larvae produced from hybrid (SJ-5 and SJ-50) and pure species crosses (SS and JJ) were sampled and analyzed using standard karyological methods and genomic in situ hybridization. In hybrid metaphase spreads, chromosomes from both parents were detected, except one metaphase, which showed the H. diversicolor supertexta haploid karyotype. The genomic composition of the hybrid was also confirmed through preliminary genomic in situ hybridization results. Many more aneuploids and chromosome fragments were found in the hybrids than those in the control pure species crosses, indicating genome instability and chromosome loss in the hybrids. In the hybrid hypodiploid metaphase spreads, two intact sets of H. diversicolor supertexta chromosomes and several H. discus discus chromosomes were detected by pairing. Spontaneous diploidization of the maternal chromosome set was shown to occur in hybrid larvae, as 2.2% heterogeneous triploid and 17.9% hypodiploids with two intact H. diversicolor supertexta chromosome sets for SJ-5. The current findings suggest that uniparental chromosome elimination along with spontaneous diploidization of maternal chromosome sets may be the reason for allogynogenesis production in H. diversicolor supertexta × H. discus discus hybridization.