Phenolic compounds are secondary metabolites that occur naturally in all plants. Seeds are among the richest organs of plants in phytochemicals, vitamins and minerals. These compounds and their biological activities are of great importance for human health. This study aimed to analyze the phenolic composition and their antioxidant activity in the seeds and epicarps of six Algerian populations of Pistacia atlantica Desf. subsp. atlantica growing along an aridity gradient from semi-arid to Saharan environmental conditions. Higher phenolic contents were observed in epicarp compared to seeds whatever the ecotype. The highest phenolic content of seeds and epicarps was observed in ecotype of Djelfa and the lowest values in Tiaret (T-Z). Phenolic composition, measured by reversed-phase high-performance liquid chromatography (HPLC), showed that quercetin in epicarp, gallic and chlorogenic acids in seeds were the most present in all ecotypes. Large differences were observed between ecotypes for nutritional values. Seeds were rich in flavonoids, proteins, carbohydrates and essential elements such as potassium, calcium, phosphorus and iron. These results highlighted the potential importance of Atlas pistachio fruits as a source of essential compounds that contribute to human health. Moreover, this underused species may serve a potential source for antioxidant components for alimentation and cosmetics purposes.