The effect of extraction methods using water, acid, Alcalase and Cellulase was studied on structure bioactivity relationship of alginates from Colpomenia peregrina. Enzyme-assisted extractions produced alginates with the lowest protein (< 0.7%) and polyphenol (< 5 mg gallic acid/g sample) contaminations. The molecular weight (M-W) of alginate extracted after acid treatment was 386.4 x 10(3) g/mol. The minimum M-W of 247.9 x 10(3) g/mol was determined for alginates extracted after Cellulase treatment. The specific volume of gyration (SVg) increased to > 0.57 cm(3)/g in enzymatically treated alginates. Alginate isolated after Cellulase treatment was nontoxic and stimulated RAW264.7 macrophage cells to release nitric oxide and inflammatory cytokines such as TNF-alpha, IL-1, IL-6, IL-10 and IL-12. The DPPH radical scavenging activity and reducing power were shown to be the highest for enzyme-treated. This study demonstrates the lab scale feasibility of extraction of alginate with the highest immunomodulatory and antioxidant properties.