Double‐flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants including peach, a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double‐flower phenotype in peach, we focused on the dominant Di2 locus. High‐resolution linkage mapping in 5 segregating progenies delimited Di2 to an interval spanning 150,858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic re‐sequencing data from single‐ and double‐flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double‐flower trait and showed transcript expression for both wild‐type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co‐segregated with the phenotype in 621 progenies accounting for the dominant inheritance of the Di2 locus. Further corroborating results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double‐flower roses. Phylogenetic analysis showed that these two genes belong to a TOE‐type clade not represented in Arabidopsis, indicating divergence of gene functions between AP2‐type and TOE‐type factors in Arabidopsis and other species. Identification of orthologous candidate genes for the double‐flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.