Abstract: The traits of flower types are one of the significant ornamental features of Camellia japonica. In order to reveal the structural characteristics of the SEP genes in Camellia japonica and its relationship with the double-petal flower type, the homologous cloning combined with RACE method was used to clone the SEP genes of Camellia japonica, and their bioinformatics analysis was performed. Then, the expression characteristics of SEP genes in different flower types of Camellia japonica were detected by the real-time fluorescence quantitative PCR. The results showed that three SEP genes were cloned from Camellia japonica Yanzhimudan, including CjSEP1a (1235 bp), CjSEP3 (967 bp), and CjSEP4a (1725 bp）. The GenBank accession numbers were OP172861, OP172863 and OP172864, respectively. These genes encoded the proteins consisting of 249, 185 and 243 amino acids, respectively. The proteins encoded by the three SEP genes of Camellia japonica were unstable, hydrophilic and localized in the nucleus, featuring conserved domains of MADS-box and K-box, and had high homology with the SEP genes of tea plants of congeneric species. The qPCR analysis indicated that the expression levels of the three SEP genes in the fully double-petal cultivar Yanzhimudan were significantly higher than those in other cultivars, followed by the semi-double-petal cultivar and the single-petal cultivar. The expression levels of SEP genes in three other specific double-petal cultivars were generally lower. Therefore, as the prominence of double-petal phenotype increased, the expression of SEP genes was up-regulated. A strong relationship existed between CjSEP genes and the characteristic double-petal trait in Camellia japonica, with different CjSEP genes exhibiting synergistic effects in their expression.