Cold-pressed pomegranate seed oil (PSO) is a product of the extraction of non-edible pomegranate seeds. Its unique chemical composition in terms of both polyunsaturated fatty acids, especially punicic acid (PA), and secondary metabolites, such as phytosterols, tocopherols and phenols, make it an interesting functional ingredient for food enrichment. It is not clear if the biomarkers profile of PSO depends to factors connected to the geographical origin of seeds. This work presents a statistical comparative analysis, concerning biomolecules composition and geographical origin of 32 commercial cold-pressed PSOs, performed by principal component analysis. The study discriminates between Turkish and Italian PSOs, on the base of the fatty acid profile and phytosterols, and not on the tocopherols and phenols. These results confirmed PA as the main characteristic biomarker of oil genuineness and, for the first time, disclosed a statistically relevant variability of phytosterols, which can be proposed as quality biomarkers for discrimination of geographical origins.