The content of carotenoids and retinoids was compared in the eyes of two Finnish populations of the opossum shrimp, Mysis relicta, which have been reproductively isolated for at least 9000 years: one from the deep, dark, Lake Pääjärvi, the other from the Baltic Sea (Pojoviken Bay). The eyes of the lake population (LP) are highly susceptible to light damage, while those of the sea population (SP) are more resistant. Carotenoids are known to act as antioxidants protecting cells against free radicals and reactive oxygen species; retinoids, on the contrary, may be phototoxic in certain conditions. Analyzed by spectrophotometry and HPLC, the carotenoid content was broadly similar in the eyes of the two populations as regards both total amount and relative proportions of more than 20 components. Noteworthy differences were found in only three of the major components, among these astaxanthin, which was two times higher in SP compared with LP. The most interesting finding was the 1.6-fold higher content of retinoids in LP compared with SP, with retinol as the dominant component (40% of total) in both populations. Retinol is a precursor of the visual-pigment chromophore retinal. The result is consistent with the idea that animals inhabiting extremely dim light environments, where very little photoregeneration of metarhodopsin to rhodopsin can occur, need a large store of chromophore (or precursors) for effective “dark” regeneration of visual pigment. We suggest that almost all the rhodopsin is then in the native state and massive pigment activation following exposure to stronger light may trigger photoreceptor damage. If such animals are handled without due light protection, e.g., when transferred to a new habitat or collected for biological experiments, their vision will be severely impaired.