► Olive tree genetic profiles and quality of monovarietal olive oils data are compared. ► Some fatty acids are highly correlated with the genetic matrix. ► Organoleptic profiles evidenced differences for the “pleasant flavours”. ► Fatty acids selected seems to represent a possible tool for monovarietal traceability. The relationship between genetic diversity and phenotype in olive, instrumental to improve the efficacy of olive clonal selection, is still far from being fully understood. This work reports on a comparison made between plant SSR genetic data and quality of monovarietal olive oils. Nine monovarietal oils produced by selected genotypes were characterised under chemical and sensory profiles. Fatty acid compositions were determined to evaluate quantitative differences among oils; some fatty acids are actually highly correlated with the genetic matrix, and PCA of fatty acids composition explains 85.53% variability. Moreover some oils characterised by high levels of oleic acid appeared interesting from a nutritional standpoint. Organoleptic profiles evidenced differences especially for the attributes defined as “pleasant flavours”; oils obtained by different genetic matrices were characterised by different flavour intensities of tomato or artichoke, almond or aromatic herbs, correspondence analysis among sensory pleasant attributes and olive oil samples explaining 91.68% variability.