The fibromelanosis (Fm) phenotype observed in both Indonesian Cemani and Chinese Silky chickens is represented by black pigmentation in skin and several organs. The mutation in the Fm region, which is located from 10.2 Mbp to 11.7 Mbp on chromosome 20, is known to be responsible for the black phenotype. The causal mutation is segmental duplication containing Endothelin3 (EDN3). The purpose of this study is to identify artificial selection in the Fm region and to elucidate the evolutionary history of Fm phenotypes in both Cemani and Silky chickens. We analyzed nine fragments of ~3 kb each in the segmental duplication and surrounding region of Cemani, Silky and other domesticated chicken populations. We also analyzed the whole region covering the nine fragments using Whole Genome Sequences from each of one individual of these chickens. We found a reduction of heterozygosity in the region close to the duplication region containing EDN3 in Cemani and Silky populations. This indicates that selection has acted and reduced the variability, and this reduction is caused by selective sweeps with the target selection site. Comparison of heterozygosity and nucleotide diversity showed the distinct boundary of reduction of variability between Cemani and Silky, suggesting that Cemani and Silky have a different timing of selection. Moreover, the calculation of divergence time based on the region downstream of duplicated EDN3 showed that this duplication in Fm region has occurred ~0.0135 mya just before the chicken domestication process in China ~0.010 mya.