There are several types of eyes in morphology such as camera eye, compound eye, mirror eye, and single lens eye, and all the eye types have been evolved from the same origin, the prototype eye. Even though there are conserved genes and networks in the eye evolution, little is known about what kinds of genetic basis have been contributed to the eye diversification. It is essential for discovering genes for the morphological diversification to develop a platform of genomic and transcriptomic comparison among species. We, therefore, developed microarray that cover the genes related to development, function, and structure of molluscan eye, as an example, for the evolutionary genomic studies.