The composition of essential oils (EO) varies according to the species and cultivars, the cultivation techniques, the environment, modifying their aroma and the quality of the processed product. We evaluated the impact of rootstock, ploidy, stage of fruit development, and of mutation versus hybridization (varietal diversity) on the chemical composition and aroma profile of orange and sour orange EO. The peel and leaf essential oils (PEO and LEO) were extracted by hydro distillation, and analysed by gas chromatography coupled with a flame ionization detector and a mass spectrometry. In parallel, their aromas were characterized by different sensory analysis techniques (discriminant and quantitative). Genetic markers (SSR and SNP) were used to assess the genetic diversity of sweet and sour oranges cultivars. A SNP genetic map of orange was built via a genotyping sequencing approach (GBS) to locate the quantitative trait loci (QTLs) of aromatic compounds. Hybridization is obviously the most disturbing factor because sweet orange and sour orange are two interspecific hybrids. Very few clementine/orange hybrids reproduce an orange aromatic profile. Furthermore, mutation-based diversity generates very little variation, either aromatic or chemical composition. The stage of fruit development has also a strong influence but only when the fruits are immature (June-September). The rootstock and the ploidy level have only a weak influence on the composition and aromatic profile of orange PEO. In postharvest, the drying method induced, under the action of heat, the disappearance of compounds of the family of oxygenated monoterpenes and aliphatic aldehydes, which leads to the deterioration of the aromatic profile. All these studied factors significantly modify the oil yield. Genetic mapping located 20 quantitative trait loci of 15 compounds and EO yield, some of which were positioned in the same linkage groups. This work points to the main factors of variation and suggests improvements for better control and preservation of aroma quality.