NAC transcription factors are one of plant-specific transcription factors that participate in the regulation of plant growth and development as well as the responses to environmental stress. In relative to the in-depth study of NAC transcription factors in model plants Arabidopsis and rice, there are few related studies on NAC transcription factors in apple. In this study, to explore the role of NAC transcription factors in growth and development, as well as biotic and abiotic stress response of apple (Malus×domestica Borkh.), full-length coding sequences of 13 MdNAC genes were isolated by search for sequence homolog and RT-PCR. The obtained cDNA sequences were used as queries in BLAST P searches against NCBI. The open reading frame (ORF) and amino acid sequence were analyzed by DNAMAN 6.0, and phylogenetic tree was constructed by MEGA 6 software. The conserved domains were predicted by Pfam 26.0 and Conserved Domains in NCBI. CELLO v.2.5, PSORT and SoftBerry ProtComp 9.0 were used for predicting subcellular location. As a result, thirteen MdNAC cDNAs from ‘Zihong Fuji’ were obtained (designated MdNAC40-45, MdNAC47-53, with GenBank accession No. MG099877-MG099882, MG099884-MG099890), with sizes of open reading frame (ORF) of 639 - 1830 bp. By phylogenetic analyses, MdNAC41 was assigned to AtNAC3 group, MdNAC40, MdNAC42-43 and MdNAC45-53 were NAM group, and MdNAC44 was belonged to VND group. The subcellular localization prediction suggested that MdNAC40-45, MdNAC47-50 and MdNAC52-53 were in the nucleus, while MdNAC51 was located in the cytoplasm or nucleus. The results from array analysis indicated that thirteen MdNAC genes were expressed in all examined tissues with various transcript abundance. RNA-seq data showed that the expression levels of MdNAC43, MdNAC45, MdNAC47, MdNAC49 and MdNAC51 were induced in response to AAAP infection. qRT-PCR results showed that, under 150 mmol/L NaCl treatment, the transcription levels of MdNAC45, MdNAC47 and MdNAC52 were induced, whereas the transcription levels of MdNAC40, MdNAC48 and MdNAC51 were down-regulated in ‘Gala’ tissue culture seedlings under 300 mmol/L mannitol treatment, the transcription level of MdNAC50 was induced, while the transcription level of MdNAC41 was down-regulated. These results indicated that 13 MdNAC genes were expressed in all examined tissues, and these genes were inducible under AAAP infection, NaCl or mannitol treatment with different degrees. Taken together, these results laid a theoretical foundation to further study the mechanism of NAC transcription factor in the regulation of apple growth, development and stress responses.