Rapid Y chromosome evolution has long been linked to hybrid male sterility, but the underlying mechanism has remained elusive. A new study from the lab shows that in hybrids between Drosophila simulans and Drosophila mauritiana, key Y-linked fertility genes are misexpressed due to severe RNA splicing defects. These genes contain exceptionally large, highly divergent introns, and in hybrids, the splicing machinery fails to properly process them, generating aberrant transcripts, including back-spliced products. Together, these findings uncover a molecular link between intronic divergence and disrupted gene expression, providing a mechanistic explanation for how rapid Y chromosome evolution can contribute to reproductive isolation.