The B subfamily of ATP-binding cassette (ABC) proteins (ABCB) plays a vital role in auxin efflux. However, no systematicstudy has been done in apple. In this study, we performed genomewide identification and expression analyses of the ABCBfamily in Malus domestica for the first time. We identified a total of 25 apple ABCBs that were divided into three clustersbased on the phylogenetic analysis. Most ABCBs within the same cluster demonstrated a similar exon–intron organization.Additionally, the digital expression profiles of ABCB genes shed light on their functional divergence. ABCB1 and ABCB19are two well-studied auxin efflux carrier genes, and we found that their expression levels are higher in young shoots of M106than in young shoots of M9. Since young shoots are the main source of auxin synthesis and auxin efflux involves in tree heightcontrol. This suggests that ABCB1 and ABCB19 may also take a part in the auxin efflux and tree height control in apple.