Amphibians and fishes have pigmented cells in organs and associated membranes. Visceral pigmentation might be related to the accumulation of residual melanin. However, the visceral pigmentation functions in amphibians are little known. In this chapter, we have analyzed Neotropical anurans’ pigmented cells, and systemic responses to environmental contaminants. Anurans have two types of internal pigmented cells: melanomacrophages (MMs) and melanocytes. Our main interest is the melanin present both in melanocytes and melanomacrophages. We have found an increase in internal melanin in leptodacytilid frogs from regions contaminated with pesticides, common in habitats with agricultural activity. In these same regions the hylid species showed decrease in melanin. Through experiments in various species, we have also tested the effects of benzo[a]pyrene (BaP), another environmental contaminant, and demonstrated that BaP decreases the internal pigmentation in both types of cells. Acute exposure study with larvae in contact with herbicide showed the tadpoles’ bodies darkened. Other emerging contaminants caused an increase in the melanin and hepatotoxicity when tadpoles were exposed. In conclusion, environmental contaminants alter the internal melanin content in anurans. Thus, internal melanin is important to protect the organism against possible damage caused by environmental contaminants.