The high proportions of monounsaturated fatty acids (MUFA) represent one of the most important technological and nutritional features of olive oils. The present study details the fatty acid (FA) composition of autochthonous cultivars (Lentisca, Madural, Redondal, Rebolã, Verdeal, and Verdeal Transmontana) produced from centenarian trees during five crop years (2013–2017). Olive cultivar highly influenced the FA composition, namely, oleic acid (70.3% for Madural to 80.7% for Redondal) and palmitic acid (10.4% for Lentisca to 13.5% for Verdeal). Similarly, crop year significantly influenced the individual FA contents. Principal component analysis of FA data enabled the unsupervised classification by cultivar and, within each cultivar, by crop year. Furthermore, the levels of nine individual FAs, together with the polyunsaturated fatty acid contents, selected using the simulated annealing algorithm, allowed for their correct classification, on the basis of linear discriminant analysis, according to the olive cultivar, with an overall sensitivity of 92%, for leave-one-out cross-validation procedure. Globally, the cultivar effect superimposed that of crop year, showing that some cultivars, such as Redondal and Verdeal Transmontana, have consistently high and homogeneous proportions of MUFA, indicating that they are worth exploring in terms of future selection of cultivars that are able to produce olive oils with increased nutritional value and that are less prone to oxidation.
