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Background: Seabuckthorn fruits contains many active subtances, among them, the seabuckthorn polysaccharide is one of the main active ingredients, and exhibits diverse bioactivities. The extraction of polysaccharides from seabuckthorn fruits is the most important step for their wide applications. Ultrasound-assisted aqueous two-phase extraction (UA-ATPE) is a promising green method for extracting polysaccharides. Additionally, physicochemical characterization and antioxidant activities can evaluate the potential functions and applications in the food and medicine industries.Results: Based on the single-factor experiments, 20.70% (w/w) ammonium sulfate ((NH 4 ) 2 SO 4 ) and 27.56% (w/w) ethanol were determined as the suitable composition for aqueous two-phase. The optimum conditions of UA-ATPE obtained by response surface methodology were as follows: ultrasonic power (390 W), extraction time (41 min), liquid-to-material ratio (72: 1 mL/g), and the total yield of the polysaccharides reached 34.14 ± 0.10%, The molecular weights of the purified upper-phase seabuckthorn polysaccharide (PUSP) and the purified lower-phase seabuckthorn polysaccharide (PLSP) were 65 525 and 26 776 Da, respectively. PUSP and PLSP contained the same six monosaccharides (galacturonic acid, rhamnose, xylose, mannose, glucose and galactose), but with different molar ratios. Furthermore, PUSP and PLSP displayed certain viscoelastic property, had no triple helical structure, possessed different thermal stability, surface morphology and conformation in aqueous solution. PUSP and PLSP displayed strong antioxidant properties by the assays of scavenging ability of ABTS + •, the protection of DNA damage and erythrocyte hemolysis.Conclusion: UA-ATPE significantly increased the yield of seabuckthorn polysaccharides. PUSP and PLSP were different in many aspects, such as molar ratio, surface shape and antioxidant activities. Seabuckthornpolysaccharides possess great potential in medicine and functional foods.