Genetic studies of peach flower and fruit characteristics have important implications in breeding efforts for improving fruit quality and availability for consumer acceptance. Currently, peach breeders lack molecular tools to enhance breeding for fruit quality traits. There is a need to discover molecular markers associated with flowering and fruit quality traits for use in marker assisted seedling selection (MASS) in order to enhance the efficiency and reliability of breeding for flowering season, maturity season and fruit quality in peach. MASS for fruit quality traits eliminates the ambiguity of modeling fruit quality attributes that are measured analytically and directly selects the characters themselves. The objective of this research project was to identify SNPs and genomic region(s) that hold major loci for bloom date (BD), maturity date (MD), fruit development period (FDP), fruit mass (FM), fruit size (FS), global fruit shape (GFS), fruit firmness (FF), soluble solid content (SSC), titratable acidity (TA) and sugar to acid ratio (SSCTA) using an association mapping population consisting of 132 genotypes. Each genotype was phenotypically evaluated for each trait over 2-3 years and sequenced using the genotyping by sequencing (GBS) protocol. The phenotypic and genotypic data were used to conduct a genome-wide association study (GWAS). We were able to identify SNPs and genomic regions that were significantly associated with BD, FDP, MD, GFS, TA and SSCTA using either the MLM or GLM procedure. At least one SNP for each of these traits was identified as a candidate for use in MASS targeted at improving flowering and fruit quality traits. We were unable to detect any SNPs that were significantly associated with FF, FM, FSD and SSC. Environmental variability between years, low variation within traits and factors associated with the preciseness of obtaining measurements are likely the reasons we were unable to identify significant SNPs for these traits. The data reported here will aid peach and other Prunus spp. breeders in MASS targeted towards widening peach germplasm for maturity, fruit shape and acidity. The data will also allow for a transferable enhanced understanding of the genetic mechanisms underlying maturity, ripening and acidity in other fruit.