A water-soluble glycopeptide (PGY), fractionated and purified from the aqueous extract of the fruiting bodies of Ganoderma lucidum via two-step dialysis, anion exchange, and gel permeation chromatography, was constituted of two moieties of carbohydrate and peptide. Carbohydrate characterization with component analysis, methylation analysis, periodate oxidation, Smith degradation, enzymic hydrolysis, and IR and NMR experiments demonstrated that the carbohydrate moiety possessed a backbone of approximately 33 (1-->3)-linked beta-d-glucopyranosyl residues and side chains, at positions 6, of single alpha-l-arabinofuranosyl residues for every three Glcp residues in the main chain. On the basis of the results of amino acid composition and trypsin digestion, the peptide moiety, shown to consist of Arg, Ser, Ala, and Gly in a ratio of 1:1:2:2, exhibited the sequence of Ser-Arg-[(Ala)2(Gly)2] and was O-attached to the carbohydrate moiety via Ser. To contribute toward our understanding of the structure-activity relationship, a series of expected derivatives generated from PGY by trypsin digestion, debranching, and NaIO4 oxidation following reduction experiments, including PTC, DB-PGY, and PPP, were obtained. All of them, as well as PGY and a reference compound (butylated hydroxytoluene, BHT), were evaluated with two conventional antioxidant testing systems of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and superoxide radical scavenging and found to have their respective antioxidant activities in a concentration-dependent manner. Comparable radical-scavenging activities observed between PTC and PGY demonstrated that the removal of Ala and Gly in a peptide moiety did not result in the variation of biological functions of PGY. However, it was very interesting to note that the scavenging activity of PPP was higher for DPPH radicals, with an SC(50) value of 116.4 +/- 5.1 microg/mL, and lower for superoxide radicals, with an SC(50) value of 205.2 +/- 14.4 microg/mL, than that of PGY with corresponding SC(50) values of 133.5 +/- 5.5 and 140.5 +/- 7.7 microg/mL, and, moreover, DB-PGY displayed the weakest scavenging potency in the tested samples, indicating that the carbohydrate moiety, in particular the side chain of nonreducing end units of Araf residues as the functional region, played a vital role in the structure and antioxidant activity. In addition, compared with the SC(50) value of BHT, PGY showed lower DPPH radical-scavenging activity but possessed higher superoxide radical-quenching potency, suggesting that it could be presented as a possible new source of natural antioxidants.