In ectothermic vertebrates, visceral organs harbor melanin-containing cells. Their ability as pigment producers is nevertheless disputed. To address expression of the key genes for melanogenesis in Atlantic salmon (Salmo salar), a tyrosinase-positive leukocyte cell line (SHK-1) and skin were used to obtain full-length tyrosinase (Tyr), tyrosinase-like protein-1 (Tyrp1), and dopachrome tautomerase (Dct) mRNA transcripts. In the SHK-1 cells, two different Tyrp1 transcripts were identified, one lacking exon 1. However, only the full-length version of Tyrp1 was identified in the skin. Sequencing of Tyrp1 genomic region revealed that the two Tyrp1 transcripts might originate from two different loci, possibly a result of pseudo-tetraploidity of the Atlantic salmon genome. Expression of Tyr, Tyrp1 and Dct was investigated by quantitative real-time reverse transcriptase polymerase cain reaction showing highest expression in the SHK-1 cell line and skin, intermediate in pronephros, and negligible or absent in liver and muscle. Histological approaches were used to demonstrate melanin and revealed presence of melanized cells in skin, kidney and liver, and absence of such cells in muscle. In addition to verify melanin synthesis abilities of visceral-located cells, our results indicate loci-specific transcription differences between populations of melanin-producing cells in Atlantic salmon.