Background: Internal organs and structures of ectotherms have melanin-containing cells that confer coloration to them. Several studies have analyzed the developmental origin, role in immunity, and hormonal regulation of these cells. However, little is known about how environmental variables influence the distribution and quantity of organ coloration. Internal melanin protects organs against environmental fluctuations. Therefore, it may influence species distribution throughout space. Here, we addressed how environmental variables (temperature, UV, and photoperiod) influence the internal coloration of anuran species after controlling for spatial and phylogenetic autocorrelations. We used the extended version of RLQ ordination that accounts for phylogenetic and spatial autocorrelation when testing for the effect of environmental variables on organ coloration in species. Results: 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 mean temperature of warmest quarter 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. Conclusion: Therefore, the amount of internal melanin seems to be a key trait influencing species distribution of anurans throughout space, since it can protect internal organs against the deleterious effect of high UV-B, temperature variation, and photoperiod.