Hexokinase (HXK) is the first irreversible catalytic enzyme in the glycolytic pathway, which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes.  However, the evolutionary pattern of the HXK gene family in apple remains unknown.  In this study, a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1.  The physiological and biochemical properties, exon-intron structures, conserved motifs, and cis-elements of the MdHXK genes were determined.  Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria, cytoplasm, and nucleus.  Gene duplication revealed that whole-genome duplication (WGD) and segmental duplication played vital roles in MdHXK gene family expansion.  The ω values of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication.  Additionally, five subfamilies were classified, and recent/old duplication events were identified based on phylogenetic tree analysis.  Different evolutionary rates were estimated among the various HXK subfamilies.  Moreover, divergent expression patterns of the MdHXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation.  Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.