Although Pax6 is required during eye development in rodents and humans, little is known about the precise role of the protein in this process. To aid in the interpretation of functional studies, we have determined the precise spatial and temporal distributions of the Pax6 protein in the eye. We find that Pax6 is initially distributed contiguously throughout a large domain of the anterior neural plate of zebrafish, including the presumptive eye fields and the dorsal diencephalon. After evagination of the optic vesicle, Pax6 becomes restricted to all proliferating cells of the pigment epithelial and neural layers of the retina. Pax6 is downregulated in most cells concomitant with differentiation. However, it remains present in several mature cell types of the eye including amacrine cells and the lens and corneal epithelia. This expression is conserved across diverse vertebrate species and suggests that Pax6 has additional conserved functions in the mature eye.