Key message : Characterization of hybrid seed failure in Prunus provides insight into conserved or lineage-specific hybrid incompatibility mechanisms in plant species. Abstract: Postzygotic hybrid incompatibility resulting from a cross between different species involves complex mechanisms occurring at various developmental stages. Embryo arrest, followed by seed abortion, is the first stage of such incompatibility reactions and inhibits hybrid seed development. In Prunus, a rosaceous woody species, some interspecific crosses result in fruit drop during the early stage of fruit development, in which inferior seed development may be accounted for the observed hybrid incompatibility. In this study, we investigated ovule development and the transcriptomes of developing ovules in inter-subgeneric crosses of Prunus. We conducted a cross of Prunus mume(subgenus Prunus), pollinated by P. persica(subgenus Amygdalus), and found that ovule and seed coat degeneration occurs before fruit drop. Transcriptome analysis identified differentially expressed genes enriched in several GO pathways, including organelle development, stimulus response, and signaling. Among these pathways, the organelle-related genes were actively regulated during ovule development, as they showed higher expression in the early stage of interspecific crosses and declined in the later stage, suggesting that the differential regulation of organelle function may induce the degeneration of hybrid ovules. Additionally, genes related to ovule and seed coat development, such as genes encoding AGL-like and auxin response, were differentially regulated in Prunusinterspecific crosses. Our results provide histological and molecular information on hybrid seed abortion in Prunusthat could be utilized to develop new hybrid crops. Additionally, we compared and discussed transcriptome responses to hybrid seed failure in Prunusand other plant species, which provides insight into conserved or lineage-specific hybrid incompatibility mechanisms in some plant species.