9-cis-epoxycarotenoid (NCED) gene is a critical gene in the pathway of abscisic acid biosynthesis. In this research, NCED gene in apple, designated as MdNCED1 (GenBank accession number: KC816734), was isolated from the apical tissue of apple rootstock SH40 (M. domestica ?M. Honanensis）by RT-PCR and RACE technology. The full cDNA was 2179bp，containing a complete open reading frame that encodes 606 amino acids. Amino acid sequence analysis revealed that the sequence had 63.7%-93.0% similarity with those of other reported plants. The ORF fragment of the gene was cloned into vector pDEST15，the recombined plasmid was transformed in to E. coli. (DE3). The result of SDS-PAGE demonstrated that the size of expected protein in the prokaryotic expression system. Fluorescent quantitative PCR analysis showed that the trend of expression of SH28, M26, SH40 and the grafted varieties ‘Gala’ were increased and then decreased. And the expression of this gene was positively associated to the dwarfing degree.