Volatile organic compounds (VOCs) are funda-mental elements of flavor, one of the most important fruit-quality traits. Despite its importance, this aspect is still poorly considered in assisted breeding programs, due to the lack of suitable and fast detection systems as well as validated func-tional markers. In this work, a full-sib parental mapping population ('Fuji×Delearly') was initially employed to per-form a comprehensive quantitative trait locus (QTL) survey, to assess the VOC segregation detected by a novel proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS) on fruit collected after a 2-month period of posthar-vest storage. Among this set of genomic regions, on chromo-some 2 was also verified the coincident location between a group of QTLs, mainly associated to esters and alcohols, with a functional marker designed for Md-AAT1, a gene involved in the last step of the ester biosynthetic pathway. The allelic effect of this marker (here named Md-AAT1 SSR) was further validated by candidate gene association mapping approach in a collection of 124 apple accessions. In this case, the volatile profiling was performed on peeled fruit flesh, as an important fraction of the aromatic blend of apple is released only after cutting. This work proposed a new and fast method for aroma phenotyping as well as a novel marker for an easy and widely applicable apple fruit quality advanced selection. Keywords Fruit quality . Volatile organic compounds . Apple flavor . QTL analysis . Candidate gene-based association mapping Introduction