The CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are critical for stem cell homeostasis in plant shoot and root apical meristem. Although CLE genes have been reported in numerous plants, there is limited information for apple. Here, twenty-five MdCLE genes were identified from apple genome (Apple Genome V1.0 predicted peptides). Analysis of chromosomal location showed that the 25 MdCLE genes were located on 12 of 17 apple chromosomes. Genetic structure analysis showed that 21 of 25 the MdCLE genes were intron-free. Expression patterns showed that most of the MdCLE genes showed higher expression levels in leaves and root compared with the other tissues. In addition, expression analysis demonstrated that MdCLE genes had different gene expression patterns for abiotic stress treatment, suggesting their potential roles in acclimation of apple to adverse environments. The 25 MdCLE genes encoded 19 different CLE peptides, and they were divided into two groups depending on their effects on the inhibition of Arabidopsis root growth. Our results suggest that MdCLE genes may have an important but redundant function in regulating plant growth and development, and this work provides valuable references for further investigation of the biological functions of MdCLE genes.