PHYTOCHEMICAL analysis of the mesocarp of eleven morphologically different individuals of Balanites aegyptiaca was assessed. The antioxidant activity of their methanol extracts was also evaluated. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) were used in combination with the metabolome detected by spectrophotometer of the evaluated individuals to distinguish between them. HCA separated the eleven individuals of Balanites aegyptiaca into three groups according to the metabolites content and total antioxidant capacity of their extracts. Group 1 is characterized with higher content of carbohydrates and lower content of other detected metabolites and antioxidant capacity. Group 2 is characterized with moderate contents of the detected metabolites, whereas Group 3 is characterized with higher contents of all detected secondary metabolites, total antioxidant capacity and strong DPPH radical scavenging. Total antioxidant capacity showed a positive correlation with total proteins, phenolics, saponins and DPPH radical scavenging activity. DPPH radical scavenging activity showed a positive correlation with total proteins, total phenolics, total flavonoids, total saponins, and negatively correlated with total carbohydrates. To our knowledge, this is the first report underlying the metabolomics of morphologically different B. aegyptiaca fruits using metabolome combined with multivariate data analysis.