Melanin is the key functional ingredient of silky fowl that has nutritional and medicinal benefits. Chishui silky fowl has unique black feather, black skin, green shell egg and black claws, while the melanin deposition of main tissues in the Chishui silky fowl remains unknown. This study aimed to investigate the pigmentation in four tissues of Chishui silky fowls compared with Taihe silky fowl from the lightness value of different tissues black degree, melanin content and the mRNA expression levels of pigmentation related genes such as ASIP, MC1R, MITF, TYR and TYRP1 by using colorimeter, enzymatic hydrolysis and RT-PCR, respectively. The results revealed that the lightness values of the chest muscle and liver, and the melanin content of leg muscle in the Taihe silky fowl were significantly higher than Chishui silky fowl hens (P < 0.05). Compared with Chishui silky fowl, the mRNA expression levels of MITF, TYR and TYRP1 were significantly upregulated in the skin of Taihe silky fowl (P < 0.05). In conclusion, the comparative analysis from lightness value, melanin content and mRNA expression levels of pigmentation-related genes indicated that Chishui silky fowl has equivalent pigmentation in the skin, muscles (chest and leg) and liver compared with Taihe silky fowl.