Within single species of stomatopod crustaceans, visual pigment classes of homologous photoreceptors throughout the retina are identical in all individuals and do not vary with the spectral characteristics of local habitats. We examined whether spectral sensitivities of stomatopod photoreceptors are differentially tuned through variations in the filter pigments associated with particular receptor classes. All classes of intrarhabdomal filters were characterized using microspectrophotometry in retinas of three stomatopod species, Haptosquilla trispinosa, Gonodactylellus affinis, and Gonodactylopsis spongicola, comparing individuals of each species collected from shallow or deep water. Depending on the depth of collection, filters varied among individuals both in optical density and in spectral shape, and the variation that was observed was similar in all three species. The changes in filter density and spectrum increased absolute sensitivity in retinas of animals living at greater depths, and tuned their long-wavelength photoreceptors for improved function in the bluer light available in deep water. Plasticity in retinal spectral function may be common in mantis shrimp species that occupy a range of habitat depths.