Abstract: CLE gene family, some members of which are related with crop yield, plays vital roles in plant growth and development. Studying of CLE genes is helpful to promote the yield of Gardenia jasminoides. Based on the genome and transcriptome data of G. jasminoides, the CLE genes were identified, and phylogenetic analysis of CLE proteins was analyzed. The expression of G. jasminoides CLE genes in different tissues and Botryosphaeria dothidea-infested leaves was analyzed using transcriptome data. A total of 23 GjCLE genes, including 6 new annotated ones, were identified, and the corresponding proteins were divided into 7 groups according to the topology of phylogenetic tree. Both GjCLE5 and GjCLE6 in group Ⅳ had a N-terminal signal peptide and might function as CLAVATA3. Gene expression analysis indicated that GjCLE5 was expressed in different tissues, while GjCLE6 was only detected in B. dothidea-infested leaves. It was primitively speculated that both GjCLE5 and GjCLE6 were candidate genes for carpel number in G. jasminoides fruit, and GjCLE6 might be the key candidate gene.