ISAFRUIT is a European integrated project aimed at increasing fruit consumption with the goal to improve health of the European citizens. One of the objectives of the work package GENFRUIT is to set the genetic basis of fruit quality by mapping the major genes and QTLs involved (Work package 6.1). This is performed on two peach (Prunus persica L. Batsch) and two apricot (Prunus armeniaca L.) progenies. Only results obtained on one of the two peach progenies, the F2 progeny of 207 hybrids issued from the ‘Ferjalou’ Jalousia® x ‘Fantasia’ cross (JxF), will be described in this paper. This progeny is segregating for six Mendelian traits, peach or nectarine (G), flat or round fruit (S), non-acid or acid fruit (D), clingstone or freestone (F), male sterility (Ps), no fruit at maturity (af), as well as for quantitative characters involved in fruit quality. This progeny was evaluated for various characters such as blooming and maturity date, fruit fresh, and dry weight, flesh firmness, juice soluble solid content; pH and acidity. The quantification of the flesh concentration in 15 to 20 major metabolites (glucose, fructose, sucrose, citrate, malate, major amino acids, and some major secondary metabolites) was performed in Bordeaux using proton NMR spectroscopy of polar extracts. Phenolics profiling, using HPLC-DAD, was performed in Avignon. Candidate genes involved in fruit sugar or acid contents and fruit development were bin mapped in the reference map ‘Texas’ x ‘Earlygold’ and in JxF. Preliminary results on QTL detection concerning fruit quality characters are presented. First colocalisations of QTLs with candidate genes were identified. In the future, the colocalisation of QTLs with candidate genes, and the colinearity of QTLs detected on the different populations analyzed in the ISAFRUIT project will be examined.