Eyes are the preeminent source of sensory information for the brain in most species, and many features of eyes reflect evolutionary solutions to particular selective pressures, both from the nonbiological environment and from other animals. As a result, the evolution of eyes, among all the sense organs, has attracted considerable attention from scientists. Paired eyes in the three major phyla, vertebrates, arthropods and mollusks, have long been considered to be classic examples of evolutionary convergence. At the macroscopic level, this must be true since they arise from different tissues and have evolved radically different solutions to the common problem of collecting and focusing light. However, opsin, the light-absorbing receptor protein, has a significant amount of shared DNA sequence homology across the phyla, and recently it has been discovered that some part of ocular development in different phyla is coordinated by a homologous, gene, Pax-6. So, although eyes from diverse phyla are clearly not homologous, neither can they be viewed as resulting solely from convergence. Instead, this shows that homology at the molecular level of organization does not predict homology at the organ or organismic level. The presence of homologous constituent molecules in nonhomologous structures reminds us that molecules are not eyes.