Animal flavoproteins called cryptochromes (CRYs) are generally believed to have distinct circadian clock functions in insects and mammals. We have discovered that the monarch butterfly, Danaus plexippus, has two cry genes: one encodes a fly-like protein with photosensitive properties, while the other encodes a mouse-like protein with potent transcriptional repressive activity. Database searches show that other non-drosophilid insects also have two cry genes. These findings change our view of how some insect clocks may work and redefine the evolution of animal CRYs.