THE Origin of a new diploid species via hybridization is theoretically difficult because it requires the development of reproductive isolation in sympatry. In the absence of isolation, the hybrid genotype will be overcome by gene flow with its parents. According to genetic models(1-3), reproductive isolation can be facilitated by rapid karyotypic evolution in the recombinant hybrid. Here we use comparative linkage mapping(4,5) to demonstrate extensive genomic reorganization in the hybrid species Helianthus anomalus, relative to its parents H. annuus and H. petiolaris. The unprecedented detail provided by the linkage maps indicates that rapid karyotypic evolution in H. anomalus results from the merger of pre-existing structural differences between the parents, as well as chromosomal rearrangements apparently induced by recombination. Moreover, determination of the parental origin of mapped loci in H. anomalus suggests that parental genomic structure has influenced hybrid genomic composition by protecting several large linkage blocks from recombination during speciation. These mapping data, when combined with previous meiotic analyses(6) and evidence of semisterility between the hybrid and its parents(6,7), satisfy genetic models for speciation through hybrid recombination.