Abstract: This study developed a method for discriminating between Andean indigenous crops and hybrid crops, using total lipid composition, fatty acid profiles, and statistical comparison. Cluster analysis and Principal Component Analysis (PCA) revealed the standard fingerprints of the gas chromatography-FID and the primary fatty acids related to loadings, which shows the explained variance (91.4–99.5%) of the total 32 cultivars, including quinoa (Chenopodium quinoa), amaranth (Amaranthus), and triticale (X Triticosecale), collected from Brazil, Bolivia, Peru, and Argentina. The primary fatty acids found in quinoa, amaranth, and triticale were linoleic (essential PUFA) (36.59–63.04 g 100 g-1), oleic (11.95–36.95 g 100 g-1), and palmitic (essential MUFA) (9.40–20.20 g 100 g-1). All grains presented four groups with the PCA method, with the exception of amaranth, with three groups. Analysed separately, linoleic and eicosenoic acids are related to quinoa; stearic and palmitic acids to amaranth; and linolenic and oleic acids to triticale Ver menos