Simple Summary: The genetic background of color is a very complex issue in both birds and mammals. Color-related genes may be represented by multiple alleles and show many interactions. Black chicken breeds are special due to their solid uniform pigmentation, which in the case of Ayam Cemani also concerns the bones and skin. One of the crucial genes involved in the melanogenesis pathway is MC1R (melanocortin 1 receptor). It is a one-exon gene that has been already studied in many different species and breeds. In the case of chicken breeds, there are numerous alleles of MC1R and they have a significant impact on the final plumage color of the individual. Here, the Ayam Cemani MC1R complete coding sequence is characterized for the first time. A new MC1R missense substitution has enabled us to distinguish a new haplotype/extended black allele. This is important in terms of completing and supporting current knowledge concerning the genetic background of plumage control, as well as in relation to describing genetic diversity between different breeds. Abstract: Plumage color is one of the most important traits characterizing chicken breeds. Black- boned chickens constitute a specific group of breeds with a unique phenotype. One of the represen- tatives is the Indonesian Ayam Cemani. The extraordinary black phenotype results from a specific chromosomal rearrangement. We used complete CDS of crucial color-related gene MC1R, which plays a key role in melanin distribution but has not been previously studied in Ayam Cemani. It turned out that Ayam Cemani individuals possess a newly found non-synonymous mutation G355A resulting in amino acid substitution D119N. Together with the presence of G274A (E92K), the new missense variant enabled us to distinguish a new extended black allele at the E locus. All of the investigated birds were heterozygous in terms of the new mutation. Previous studies and our own results indicate a high level of genetic variation within the MC1R gene within and between chicken breeds. Besides the key mutations that make it possible to distinguish particular major alleles, there are also numerous substitutions that give haplotypes more characteristics for individual breeds.