In theory, selection for effective camouflage (i.e. dull coloration) in fish should be strongest when the conditions for visual predation are most favourable, such as in structurally simple pelagic habitats. By contrast, in more sheltered (e.g. littoral) habitats, selection may favour effective intra-specific communication (i.e. bright coloration) (at the expense of crypsis). Poor transparency, as in highly humic waters, should constrain colour adaptations. We investigated phenotypic variation in body coloration of Eurasian perch (Perca fluviatilis L.) in littoral and pelagic habitats of four humic boreal lakes. Perch from the most transparent lake had the lightest and less coloured belly and perch were more colourful in the littoral habitats than in the pelagic areas, with the pattern being clearest in the most transparent lake. In addition, perch in the most transparent lake exhibited sexual dichromatism, with males having a more colourful belly than the females, whereas no indications of sexual dichromatism were found in more humic lakes. Moreover, in the most transparent lake, the condition of fish correlated with bright belly coloration in the littoral, but with dull belly coloration in the pelagic habitat. The results obtained in the present study suggest that selection on perch coloration may differ between lakes as a result of visual properties of the water, and within lakes as a result of divergent selection for camouflage and communication in pelagic and littoral habitats. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 47–59.