Rearrangements of the visual pigment genes are associated with defective color vision and with differences between types of red-green color blindness. Among individuals within the most common category of defective color vision, deuteranomaly, there is a large variation in the severity of color vision loss. An examination of specific photopigment gene sites responsible for tuning photopigment absorption spectra revealed differences that predict these variations in the color defect. The results indicate that the severity of the defect in deuteranomalous color vision depends on the degree of similarity among the residual photopigments that serve vision in the color-anomalous eye.