Fruit tree breeding is deeply involved in the selection of new varieties that have to be adapted to climate changes but also have to withstand the different pathogens that sometimes are spread at global level. There is, therefore, an urgent need to accelerate the selection methods to contribute to a sustainable production with a reduced environmental impact but that takes also into account the primary objective of product quality. To meet these challenges, today’s breeders have access to powerful new tools to simplify the selection of new varieties, tools that integrate high-throughput genomic technologies and tools for precision phenotyping to better analyze the genetic diversity of agricultural species as never before. A gradual cost decrease in recent years has allowed the sequencing of the genomes of more than fifty species about ten of which widely used for fruit production such as grape, apple, strawberry, peach, Chinese and European pear, banana, kiwifruit and several species belonging to the Citrus genus. Consequently it is possible at present the re-sequencing of different varieties for many species with the Next Generation Sequencing (NGS) techniques. This approach has also simplified the identification of genes of agricultural interest and the characterization of large genomic regions that control quantitative traits (Quantitative Trait Loci or QTL). This last aspect is very important because of the polygenic nature of most of the fruit quality traits (fruit size and shape, firmness, organic acid and sugar contents among the others). This paper describes the most important results achieved after the beginning of the genomic era and gives an overview on the first genes, related with quality traits, identified thanks to the availability of the sequenced genomes. different mutations on a CCD4 gene resulted in the determination of the yellow flesh of peaches. This gene encodes for a Carotenoid Cleavage Dioxygenase, that has the role of carotenoid degradation. The functional allele of the gene is responsible of the white phenotype while the yellow one can be found only in varieties that present two mutated alleles at this locus. A second trait for which genes have been identified is related to maturity date in peach. The peach sequence genome availability made it possible to identify a NAC gene in a very narrow genomic region controlling maturity date. An in-frame insertion of 9 bp in the last exon of this gene perfectly co-segregated with the maturity date locus in two large peach F2 populations. The G locus for the peach/nectarine phenotype of the peach fruit skin has been characterised by using an integrated approach with fine mapping and deep resequencing of varieties with peach or nectarine phenotype. The fine mapping approach made it possible to reduce the region in which to identify the gene controlling the G locus. The resequencing approach was tempted in order to identify all the gene variants for the 25 genes found in this region. It was possible to demonstrate that the insertion of a large retrotransposon in MYB transcription factor resulted in the nectarine phenotype and that a unique mutational event gave rise to the nectarine trait. All the markers developed in these three papers are already available for MAS in peach. Synteny among the Prunus species genomes makes it possible to use the peach genome sequence for studies in related species such as sweet cherry, apricot, plum and almond. This approach was used to identify and characterise the CNR (Cell Number Regulator) gene family in sweet cherry. The high expression of these genes inhibits cell division in the early stages of fruit development. Two members of this family are located in two QTL regions for fruit size in cherry and two less efficient allelic variants (with small sequence polymorphisms in the promoter region) of the PavCNR12 member are linked with a consistent increase of fruit size. The last example is the case of the transcription factor of the MYB family responsible of the anthocyanin accumulation in fruit skin and flesh of apples. These genes have been characterized before the availability of the apple genome sequence but in the last years several new allelic variants mainly for red-fleshed apple have been identified and new parental lines for apple breeding have been taken into account. The recent interest on research on fruit anthocyanins is derived from their potential benefits on human health, especially for their anticancer, anti-inflammatory and cardioprotective properties. We are just at the beginning of this new era and it is reasonable to think that gene identification will become easier and cheaper so allowing the transfer of the molecular knowledge to breeding practices.