The relationship between molecular structure and bioactivity was evaluated for alginates obtained under different extraction methods (water, acid, alcalase and cellulase) from Sargassum angustifolium. The use of enzymes considerably reduced protein (from 14.58% to <0.4%) and polyphenol (from 16.0% to <1.7mg GA/g sample) contaminations of alginates compared to those of water and acid. The FT-IR spectrum revealed that extraction method did not affect the structure of the recovered alginates. The highest molecular weight (Mw) (557.1×103g/mol) was found in acid treated alginate while the Mw of cellulase assistant alginate (356.2×103g/mol) was the minimum. The SVg values varied from 2.79–5.17cm3/g revealing the loosed conformational structures of alcalase and cellulase assistant alginates. Alcalase assistant alginate stimulated RAW264.7 cells to release nitric oxide and inflammatory cytokines TNF-α, IL-1, IL-6, IL-10 and IL-12. Enzyme treated alginates showed maximum DPPH radical scavenging activity and reducing power. Therefore, the present results showed the determinant effect of pretreatment during the extraction process of alginate and the beneficial influence of enzymatic process when biological functions of alginates are of high interest in the industry.