Quality control and traceability of Argan oil requires precise chemical characterization considering different provenances. The fatty acid profile is an essential parameter that certifies the quality and purity of Argan oil. In addition, stable isotopes were recently shown to be accurate as an indicator for geographical origin. In this study, fatty acid composition by gas chromatography (GC) and stable isotope ratio by isotope ratio mass spectrometry (IRMS) were investigated for classifying Argan oil according to its geographical origin. Forty-one Argan oil samples, belonging to six geographical origins of Moroccan natural Argan population (Safi, Essaouira, Agadir Ida Outanane, Taroudant, Tiznit and Sidi Ifni) were collected and extracted under the same conditions. The results show that the isotope δ13C, palmitic acid (C16:0), linoleic acid (C18:2) and unsaturated fatty acids (UFA) were strongly influenced by ecological parameters. Linear discriminant analysis (LDA) was performed to discriminate the six studied provenances. Discriminant models predicted the origin of Argan oil with 92.70% success. Samples from Safi, Essaouira and Agadir Ida Outanane presented the highest classification rate (100%). In contrast, the lowest rate was reported for samples from Tiznit (85.70%). The findings obtained for fatty acids and isotope combination might be considered as an accurate tool for determining the geographical origins of Argan oil. Moreover, they can potentially be used as specific markers for oils labeled with Protected Geographical Indication (PGI).