In photoreceptor cells, light activates visual pigments consisting of a chromophore (retinal) and a protein moiety (opsin). Activated visual pigments trigger an enzymatic cascade, called phototransduction cascade, in which more than ten phototransduction proteins are participating. Two types of vertebrate photoreceptor cells, rods and cones, play roles in twilight and daylight vision, respectively. Cones are further classified into several subtypes based on their morphology and spectral sensitivity. Though the diversities of vertebrate photoreceptor cells are crucial for color discrimination and detection of light over a wider range of intensities, the molecular mechanism to characterize the photoreceptor types remains unclear. We investigated the amino acid sequences of about 50 vertebrate opsins, and found that these sequences can be classified into five fundamental subfamilies. Clear relationships were found between these subfamilies and their characteristic spectral sensitivities. In addition to opsins, we studied other phototransduction proteins. The amino acid sequences of phototransduction proteins can be classified into a few subfamilies. Even though their spectral sensitivity is considerably different, cones fundamentally share the phototransduction protein isoforms which are different from those found in rods. It is suggested that the difference in phototransduction proteins between rods and cones is responsible for their sensitivity to light. Isoforms and their selective expression may characterize individual photoreceptor cells, thus providing us with physiological functions such as color vision and daylight/twilight visions.