Anatomically widely different designs of animal eyes have long been thought to arise independently multiple times during evolution. This morphology-based view has been challenged by the identification of a highly conserved transcription factor Pax6 that plays a key role in eye development in both flies and mammals. The origin of Pax genes predates the origin of eyes and the nervous system since a PaxB-like gene, belonging to the Pax2/5/8 gene subfamily, was identified in sponge lacking nervous system. Structurally similar PaxB gene is implicated in visual system development in jellyfish, the most basal organism possessing complex eyes. The widespread use of Pax genes in the genetic program underlying eye formation throughout the animal kingdom raises a question why certain transcription factors have been frequently redeployed to build eyes. A model is proposed that provides a plausible explanation for the apparently ancient role of Pax genes in eye evolution.