Two large molecular weight fucoidan fractions F-A and F-B were obtained by water extraction and anion-exchange chromatography and then L-A and L-B with low molecular weight and uronic acid content were prepared by radical process degradation of F-A and F-B. The antioxidant activities of the fucoidan fractions on two oxygen free radicals and Cu2+-induced low-density lipoprotein (LDL) oxidation were studied. The results show that all the fucoidan fractions had excellent scavenging capacities on superoxide radical and hypochlorous acid, except the highly sulfated fraction L-B. In LDL oxidation system, low molecular weight fractions L-A and L-B exhibited great inhibitory effects on LDL oxidation induced by Cu2+, however F-A and F-B had little inhibitory effects in this system due to their large molecular weights. The present results suggest that fucoidan from Laminaria japonica is an excellent natural antioxidant and has great potential for preventing the free radical-mediated diseases.