Abstract Ethylene is a gaseous hormone that coordinates several important physiological processes resulting in the final fruit quality in apple. Due to its genetic heterozygousity, apple offers the possibility to exploit the natural allelic variation existing at the level of two genes involved in the ethylene biosynthetic pathway, Md-ACS1 and Md-ACO1. The allelism of these two genes can be exploited for the advanced selection of genotypes characterized by low ethylene production, with a consequent extended postharvest storability. The impact of these two elements in ethylene control was verified using two specific apple populations (‘GDxBr’ and ‘FjxMG’) presenting distinct allelotype configurations. In the first progeny, two QTLs were identified in genetic positions corresponding with these genes, and for the first time the association of a QTL for ethylene production with Md-ACO1 in apple was established. However, the analysis carried out on the second population, homozygous for the allele of Md-ACS1 associated with a low ethylene production, suggested the possible involvement of other genetic elements in the regulation of ethylene production. In the end we also present, in parallel to the GC assessment, a novel methodology based on proton transfer reaction-time of flight-mass spectrometry (PTR-ToF-MS) for a more reliable, fast and efficient monitoring of the ethylene production in apple.