Fruit color is one of the important commercial traits of pepper. In this study, ornamental pepper GS6, Z1, sweet pepper SP01 and its yellow mutant SP02 were used as materials to explore the sequence differences and expression characteristics of capsanthin/capsanthin synthase (CCS) gene in pepper with different mature fruit colors, and to preliminarily analyze the molecular mechanism of pepper with different mature fruit colors. The results showed that the full-length CCS gene could be cloned from GS6, Z1 and SP01 with red mature color, and there was no difference in the sequence. The full-length of CCS gene was 1497 bp, encoding 498 amino acids, containing only one open reading frame sequence and no intron sequence. The CCS gene was not cloned in the yellow mutant SP02. Clustering and phylogenetic analysis showed that the CCS genes of Capsicum annuum were more closely related to Capsicum chinense, Capsicum baccatum, and Solanum pennellii of Solanaceae crops. The results of qRT-PCR analysis showed that the expression of CCS gene was the highest in flowers in GS6. In Z1 and SP01, the expression level of CCS gene in fruit was significantly higher than that in other tissues, and the expression level in root was the lowest. The CCS gene was not expressed in the stems and leaves of SP01 and all tissues of SP02. At different fruit development stages, the expression of CCS gene increased significantly at 30 days after flowering ( stage III ) of SP01, 40 days after flowering ( stage IV ) of GS6 and Z1. The results showed that the formation of fruit color of sweet pepper yellow mutant SP02 may be closely related to the deletion or variation of CCS gene, and the expression of CCS gene in mature red pepper may play an important role in fruit color formation.