Peach (Prunus persica (L.) Batsch) and sweet cherry (P. avium L.) are two Prunus species cultivated in temperate regions. In peach, many fruit quality traits are controlled by a single or a small number of genes. On the opposite, in sweet cherry, most fruit quality traits are complex. In peach, the D locus controls fruit acidity, low‐acidity is determined by the dominant allele while the S locus (for saucer peach), controls the fruit shape, flat being dominant. In sweet cherry, one of the most important fruit quality traits for producers is the fruit cracking tolerance, especially in regions where rainy springs can destroy nearly all the production. A positional cloning strategy using a large F2 population of 2161 individuals and differential expression analysis of the two parents of the F2 population (Ferjalou Jalousia and Fantasia) using RNA‐seq, lead to the identification of candidate genes for the non acid fruit trait in peach. For the S locus, positional candidate genes were identified on the basis of their functional annotation. Using two sweet cherry F1 mapping progenies, Regina × Lapins and Regina × Garnet, many QTLs were detected for fruit cracking tolerance, each of them explaining a small percentage of the observed variation. Interestingly, one of them was detected in each year of evaluation. New deeper phenotypic studies will be developed to dissect this complex character. We will compare the methodology used to study these simple and complex traits, and discuss their application in selection programs.