Abstract: CLE gene family, some members of which are related with crop yield, plays vital roles in plant growth and development. Investigation of CLE genes will help to promote yield in Gardenia jasminoides. Based on the genome data of G. jasminoides, the CLE genes were identified, and phylogenetic analysis of CLE proteins were 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 functioned as CLAVATA3. The results of expression profiling indicated that GjCLE5 expressed in different tissues, while GjCLE6 was only detected in B. dothidea-infested leaves. We primitively believed that both GjCLE5 and GjCLE6 were candidate genes to regulate fruit carpel number in G. jasminoides, and GjCLE6 might be a key candidate gene.