AP2/ERF transcription factor family is one of the most important transcription factor families in plants, which is involved in plant crucial biological processes such as growth and development, stress resistance and plant hormone signaling pathway. Based on PacBio sequencing database of M. sieversii upon the Valsa mali infection, MsAP2/ERF family members were screened and identified using the hidden Markov model of AP2 domain (PF00847). The MsAP2/ERF transcription factor family were identified and analyzed by MEGA6, NCBI CDD batch, MEME, ExPASY, BUSCA. The gene expression analysis based on RNAseq data and qRTPCR assay were performed to screen the potential resistant genes for Valsa canker disease. The main results are as follows: (1) in total, 106 AP2/ERF genes were identified in M. sieversii, including AP2 (17 genes), ERF (57 genes), DREB (25 genes), RAV (5 genes), and Soloist (2 genes). (2) Further detailed classification showed that the MsERF subfamily included 6 groups (B1-B6). The MsDREB subfamily contained A2, A4, A5 and A6 groups, and lacked A1 and A3 group genes. (3) Differential expression pattern analysis based on RNAseq data showed that 29 MsAP2/ERF genes were differentially expressed during the infection of V. mali. Among them, 19 DEGs were MsERF genes. (4) The qRTPCR results of 12 representative MsAP2/ERF genes showed that 8 MsERF genes were significantly upregulated after V. mali infection. Particularly, the B4 group of ERF subfamily gene (MsERF40) was remarkably upregulated with the highest fold increase at 5 d after the infection of V. mali compared with the control. Three MsDREB genes were significantly upregulated and one MsDREB gene was downregulated after V. mali infection. In addition, the MsERF gene containing TIR domain (MsERF05) was upregulated with 69fold increase at 1 d. Those results show the MsERF40 and MsERF05 play a key role during resisting V. mali in M. sieversii. In conclusion, this study laid a foundation for the further function and mechanism of MsAP2/ERF genes that respond to the V. mali infection in M. sieversii.