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The biological importance of fatty acids in different metabolic routes and/or specific activities with medical, cosmetic, pharmaceutical interest makes it increasingly necessary to know in detail the lipid composition of foods. The objective of this work was to identify and characterize the fatty acids profile of seven pomegranate varieties with commercial interest, differentiating between its edible (seeds) and non-edible (peel plus carpellary membranes) parts, aiming to have a holistic and characteristic vision. The results confirmed the compositional fatty acids variations of the pomegranate, both between different varieties and the parts of the fruit. 29-101 variety presents a fatty acid profile with a higher potential for antifungal, antibacterial and antiviral properties. The content of punicic acid in the Kingdom variety makes it the most pomegranate varieties interesting for its nutraceutical, pharmaceutical, food and medical applications. The specific fatty acid content could define the best pomegranate variety depending on its potential use/application.