The vertebrate ancestor possessed ultraviolet (UV) vision and many species have retained it during evolution. Many other species switched to violet vision and, then again, some avian species switched back to UV vision. These UV and violet vision are mediated by short wavelength-sensitive (SWS1) pigments that absorb light maximally (lambda(max)) at approximately 360 and 390-440 nm, respectively. It is not well understood why and how these functional changes have occurred. Here, we cloned the pigment of scabbardfish (Lepidopus fitchi) with a lambda(max) of 423 nm, an example of violet-sensitive SWS1 pigment in fish. Mutagenesis experiments and quantum mechanical/molecular mechanical (QM/MM) computations show that the violet-sensitivity was achieved by the deletion of Phe-86 that converted the unprotonated Schiff base-linked 11-cis-retinal to a protonated form. The finding of a violet-sensitive SWS1 pigment in scabbardfish suggests that many other fish also have orthologous violet pigments. The isolation and comparison of such violet and UV pigments in fish living in different ecological habitats will open an unprecedented opportunity to elucidate not only the molecular basis of phenotypic adaptations, but also the genetics of UV and violet vision.