Carotenoid-binding protein (CBP) is the only key protein that has been characterized to be involved in yellow cocoon coloration of the domesticated silkworm (Bombyx mori). Gene structure and mRNA expression profiles of cbp along with UV-Vis spectrum profiles of carotenoids in silk glands were investigated among twelve strains to disclose their relationship with cocoon color. Yellow cocoon strains of B. mori contained two or three cbp gene types, which had different mRNA products with a longer form acting functionally to code CBP protein and the smaller one without exon 2. The structures of cbp were different among the green cocoon strains with the mRNA product lacking exon 2. Only one cbp gene structure existed in white cocoon strains of B. mori, which produced the mRNA product free of exon 2. A newly identified intron 1 sequence of cbp gene in this study may have cocoon color-specificity among strains. The UV-Vis spectrum profiles of carotenoids in the yellow cocoon strains' silk glands were significantly different from those in the green cocoon strains and white cocoon strains.Together, it can be concluded that the gene structure and expression profile of cbp was closely linked to cocoon colors of B. mori.