Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as a support for homoploid hybrid speciation (HHS), a process by which a new reproductively-isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendents. We show that meiotic segregation, operating in the hybrid lineage, resulted in formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrat