Prunus genus contains species cultivated for their ornamental features, including peach and almond. Breeding of ornamental woody trees is mainly focused on selection based on morphological ornamental features. Identification of QTLs and genes associated with flower morphological traits in Prunus will facilitate to understand the genetics of flower morphology and biology. A mapping population (n=118) was developed from a cross between two peach hybrid rootstocks: ‘Adafuel’ (P. dulcis × P. persica; 2n=2x=16) and ‘Flordaguard’ (P. persica × P. davidiana; 2n=2x=16). A segregating population was genotyped by Genotyping-by-Sequencing (GBS) and a total of 18,861 SNPs were identified and used for linkage map construction. A characterization of flower morphology was carried out and the segregation patterns of the observed traits were determined. Anther color, full bloom date, petal color and shape, single/double flowers, and other morphological flower traits were mapped using MapQTL 6.0 software. Both parents have single showy flowers with five petals and the F1 progeny segregated into single and double showy flowers with a 3:1 ratio, exhibiting in the latter some extra petals or petaloids. Anther color of both parents is yellow and in the F1 progeny it segregated into yellow, orange, pale red, white, and pink with a 8:4:2:1:1 ratio. This suggests that the trait is controlled by two loci with dominant epistasis. The phenotypic segregation and the QTL identification of flower traits can be useful in ornamental scion and rootstock breeding.