Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2 , for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’ trees grafted on 1123 hybrids from ‘ M alus baccata ’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 and MdARF6 were predicted as candidate genes from Dw1 , while MdG3OX3 was a candidate gene from Dw2 . An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 and caused increased expression of MdLBD3 . Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 , leading to higher expression of MdG3OX3 . At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdABI5 and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion : The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the accurate genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that ABA, auxin, GA, and zeatin signals may be involved in the regulation of apple rootstock dwarfing mechanism.