It is known that histone acetyltransferases (HATs) are involved in a wide range of biological processes by activating gene expression. However, the regulatory role of HATs in apple remains to be elucidated. This study identified 58 HATs from the apple genome (named MdHATs) and performed comprehensive analyses of these MdHATs, given their involvements in plant development and stress response. Firstly, we classified 58 predicted MdHATs into four different categories based on the phylogenetic analyses. Then, the intron/exon structures, conserved motifs, and structural domain organization of MdHAT genes and predicted proteins were further analyzed. Next, we investigated the expression patterns of MdHATs during apple plants' development process and stress responses. Moreover, according to these findings, we selected two candidate genes, MdHAG1 and MdHAM1, and ectopically expressed them in tobacco to investigate their function in response to drought and low-temperature stress, respectively. The results showed that overexpression of MdHAG1 in tobacco negatively regulated drought tolerance and cold tolerance of transgenic tobacco, and overexpression of MdHAM1 in tobacco improved drought tolerance and cold tolerance of transgenic tobacco. In summary, our study provides a comprehensive analysis of the MdHAT family and insights into the epigenetic mechanisms of histone acetylases under abiotic stress.