The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is considered the first rate-limiting enzyme in plant isoprenoid biosynthesis. We discovered the MdHMGR4 gene in Malus domestica which showed 97.70% amino acid sequence identity with MdHMGR1. MdHMGR4 showed a root-specific expression pattern in apple and was strongly enhanced by ETH, MeJA, and SA while MdHMGR1 was expressed in a constitutive manner and was not sensitive to these hormone treatments. The MdHMGR1 and MdHMGR4 promoters were cloned, sequenced, and analyzed using bioinformatics tools. Their promoter sequence homology was 48.93% and various potential cis-acting elements responsive to hormones were present. GUS activity, driven by the full length MdHMGR1 and MdHMGR4 promoters, was observed in transgenic Arabidopsis. Plants carrying the full MdHMGR1 promoter exhibited strong GUS expression in seedlings, leaves, stems, and flowers, while significant GUS activity driven by the full MdHMGR4 promoter was found only in roots. The MdHMGR1 promoter was a constitutive promoter and the MdHMGR4 promoter was a root-specific promoter. Deletion analysis based on Agrobacterium-mediated transient assays in Arabidopsis seedlings indicated that the MdHMGR4 promoter region from -144 to + 175 could maintain the basic promoter activity for root-specific expression.