The vertebrate-type opsin, Ci-opsin1, is localized in the outer segments of the photoreceptor cells of larvae of the ascidian Ciona intestinalis. The absorption spectrum of the photopigment reconstituted from Ci-opsin1 and 11-cis-retinal suggested that the photopigment is responsible for photic behavior of the larvae. The structure and function of Ci-opsin1-positive photoreceptor cells were examined by immunohistochemistry, confocal microscopy, electron microscopy, laser ablation, and behavioral analysis. Ciona larvae have three morphologically distinct groups of photoreceptor cells in the brain vesicle. Group I and group II photoreceptor cells are associated with the ocellus pigment cell on the right side of the brain vesicle. The outer segments of the group I photoreceptor cells are regularly arranged inside the small cavity encircled by the cup-shaped pigment cell. The outer segments of the group II photoreceptor cells are located outside the pigment cavity and exposed to the lumen of the brain vesicle. The outer segments of the group III photoreceptor cells are located near the otolith on the left ventral side of the brain vesicle. Thus, the brain vesicle of the ascidian larva has two ocelli: a 'conventional' pigmented ocellus containing the group I and group II photoreceptor cells and a novel nonpigmented ocellus solely consisting of the group III photoreceptor cells. Laser ablation experiments suggest that the pigmented ocellus is responsible for the photic swimming behavior. The nonpigmented ocellus might relate to later developmental or physiological events, such as metamorphosis, because Ci-opsin1 immunoreactivity appears in the late larval stage and becomes intense just before the onset of metamorphosis.