In this study, the correlation between the color discrimination ability and the genetic polymorphism is investigated. It is known that the variation in spectral sensitivity of the L cone is common among normal color vision subjects. It is due to the genetic polymorphism in cone pigments (opsins). The 180th amino acid residue of the L cone opsin is frequently replaced from serine to alanine. It is also known that due to the replacement the wavelength of the L cone peak sensitivity shifts about 6nm to the short wavelength direction. Assuming that the neural processing in the neurons and the brain is the same for both the standard observer and the observer whose spectral sensitivity of the L cone opsin shifts by 6nm (shift observer), we designed color pairs so that the color difference between the pairs looks larger to the standard observer than to the shift observer. To extend the color difference only for one of the two observers, the four primary color display ‘Quattron’ developed by SHARP Corporation was used. The experimental results, surprisingly, showed that the subjects whose 180th amino acid residue of the L opsin is alanine could better discriminate the pairs of colors that were designed to be discriminated by the standard observer. This result may mean that the neural processing is dependent on the polymorphism, and the human color discriminability variation cannot be explained simply by the cone spectral sensitivity shift.