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Marker-assisted selection (MAS) has been little implemented in peach breeding. This was notably due to the low number of available markers, and/or to their limited transferability when crosses developed from different genetic backgrounds are used. To solve this, we have genotyped six progenies derived from twelve unrelated parents, in segregation for a set of six major Mendelian characters (five characters of the fruit and resistance to the green peach aphid), using the Infinium^® II array of Illumina containing 9000 SNPs (IPSC 9K array v1). The resulting genetic maps allowed identifying a set of SNPs strongly associated with the different phenotypic variants. Furthermore, the comparison of these results with those obtained from a genetic association study based on the same SNP array, allowed identifying a set of common SNPs, which thus provides a sound basis for the construction of haplotypes and the implementation of marker-assisted selection for these characters, in peach breeding programs.