Baleen whales (Mysticeti) such as the blue whale have lost their teeth and instead use racks of baleen to filter zooplankton and small fish from ocean waters. Previous studies with molecular data have documented inactivating mutations in tooth-specific genes that are shared by all extant baleen whales. However, the molecular changes that underpin the origin of baleen remain have yet to be elucidated. In this study we show that a small number of KRTAP hair genes have been highly amplified and repurposed as 'baleen genes' in mysticetes.