The WRKY family, a large family of transcription factors (TFs) found in higher plants, plays central roles in many aspects of biological processes and adaption to environment. However, little information is available on this family in apple (Malus domestica). In the present study, a total of 119 candidate WRKY genes in apple genome were identified and classified into three main groups (Group I-III) based on the structure of the conserved domains. Each group or subgroup showed similar exon-intron structures and motif compositions. The evolution analysis showed that 44 MdWRKY genes clustered into 20 intensive regions (<100 kb) and 78 MdWRKY formed 85 pairs of collinear relationships, suggesting that both tandem and segmental duplications played an important role in the evolution and diversification of the WRKY gene family in apple. Furthermore, the expression of the MdWRKY genes in apple leaves in response to biotic stress (Alternaria alternate) and hormone treatments [salicylic acid (SA), methyl jasmonate (MeJA) and ethephon] was examined by using RNA-seq and qRT-PCR. The results showed that 63 MdWRKY genes had differential expression in their transcript abundance in response to Alternaria alternata apple pathotype infection. Moreover, most pathogen responsive MdWRKY genes were also changed significantly when apple leaves were treated by SA, MeJA or ethephon plant growth regulations, suggesting an interaction between SA, JA and ethylene (Eth) hormone signaling under biotic stress. This work may provide the basis for future studies of the genetic modification of WRKY genes for pathogen resistance in apple.