Berries and seeds of two subspecies (ssp. sinensis and mongolica) of sea buckthorn (Hippophaë rhamnoides L.) were compared in terms of triacylglycerols, glycerophospholipids, tocopherols, and tocotrienols. The berries of ssp. mongolica contained less oleic acid (4.6 vs 20.2%, p < 0.001) and more palmitic (33.9 vs 27.4%, p < 0.01) and palmitoleic (32.8 vs 21.9%, p < 0.05) acids in triacylglycerols than those of ssp. sinensis. The proportions of linoleic acid (32.1 vs 22.2%, p < 0.01, in berries; 47.7 vs 42.7%, p < 0.05, in seeds) and palmitic acid (21.1 vs 16.4%, p < 0.001, in berries; 17.0 vs 14.1%, p < 0.05, in seeds) in glycerolphospholipids were higher in ssp. mongolica than in ssp. sinensis, and vice versa with oleic acid (4.3 vs 18.5% in berries, 10.0 vs 22.2% in seeds, p < 0.001). A higher proportion of alpha-linolenic acid was also found in the glycerophospholipids of ssp. sinensis berries (16.2 vs 10.1%, p < 0.001). alpha-, beta-, gamma-, and delta-tocopherols constituted 93-98% of total tocopherols and tocotrienols in seeds, and alpha-tocopherol alone constituted 76-89% in berries. The total contents of tocopherols and tocotrienols varied within the ranges of 84-318 and 56-140 mg kg(-1) in seeds and whole berries, respectively. The seeds of ssp. mongolica were a better source of tocopherols and tocotrienols than those of ssp. sinensis (287 vs 122 mg kg(-1), p < 0.001). The compositional differences between the two subspecies should be considered when the berries are bred and exploited for nutritional purposes.