Seventeen natural population of Seabuckthorn (SBT), which comprised 187 plants from trans-Himalaya, were studied to find out variability and genotypic effect on total phenolic content (TPC), total antioxidant capacity (TAC), ascorbic acid and carotenoids content in fruit pulp. The fruits were found to be rich in TPC ranging from 964 to 10,704 mg gallic acid equivalent/100 g. The free radical-scavenging activity in terms of inhibitory concentration (IC 50 ) ranged from 0.7 to 9.1 mg/ml and ferric reducing antioxidant potential (FRAP) from 180 to 1355 FeSO 4 ·7H 2 O μg/ml. The ascorbic acid and carotenoids content ranged from 56 to 3909 mg/100 g and 0.1–14.4 mg/100 g, respectively. A variation of 1–11 fold in TPC, 1–14 folds in IC 50 by 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay and 1–8 fold in ferric reducing antioxidant potential, 1–70 fold in ascorbic acid content and 1–206 fold in carotenoid content among the examined fruit across 17 populations underlines the important role played by genetic background and the geographical location for determining the health promoting compounds. Significant correlation was observed between TPC, IC 50 , FRAP, carotenoids, ascorbic acid, fruit lightness (L*) and plant height. Among the 20 morphological traits studied, fruit colour and plant height showed positive correlation with the health promoting compounds.