SummaryInternal organs of ectotherms have melanin-containing cells. Several studies analyzed their developmental origin, role in immunity, and hormonal regulation. However, little is known about how environmental variables influence the distribution and quantity of organ coloration. Here, we addressed how environmental variables (temperature, UV, and photoperiod) influence the internal coloration of amphibians after controlling for spatial and phylogenetic autocorrelations. Coloration in all organs was correlated with phylogeny. However, the coloration of the heart, kidneys, and rectum of hylids, R. schneideri, some Leptodactylus, and Proceratophrys were influenced by temperature and photoperiod, whereas that of the testicle, lumbar parietal peritoneum, lungs, and mesenterium of Leiuperinae, Hylodidae, Adenomera, most Leptodactylus were influenced by UVB and temperature variation. Therefore, the amount of internal melanin seems to be a key trait influencing species distribution of frogs throughout space, since it can protect internal organs against the deleterious effect of high UV-B, temperature variation, and photoperiod.SignificanceThe functions of internal coloration in fishes and frogs are little known. Internal pigmentation is commonly altered in fish and the degree of response is correlated with body transparency levels, suggesting possible adaptive functions. Here, we assume that internal melanin has protective functions against UV-B, temperature variation, and photoperiod. Thus it could influence frogs species distribution throughout space. The melanin coloration of each organ was influenced by distinct environmental variables depending on the lineages of species. Our results could direct further studies about the functions of internal coloration.