A novel heteropolysaccharide (GCPB-2) with a molecular mass of 1.03 × 105 Da was isolated from the submerged fermentation culturing mycelia powder of Lingzhi, Ganoderma capense, by DEAE-52 cellulose, DEAE Sepharose CL-6B, and Sephadex G-75 column chromatography. Its chemical structure was characterized for the first time. The antioxidant activity was evaluated by two antioxidant assay methods. The result of this study introduced G. capense as a possible valuable source that helped to exhibit some antioxidant properties. The homogeneous polysaccharide was composed of xylose and arabinose in the molar ratio of 1:1, and showed a specific optical rotation of [α]D25 = +161° (c 1.0, H2O). Monosaccharide analysis, partial acid hydrolysis, periodic acid oxidation, methylation analysis, gas chromatography-mass spectrometry (GC-MS), Fourier transform-infrared spectroscopy (FT-IR), and nuclear magnetic resonance (NMR) spectroscopy (1H, 13C, HMQC and HMBC) were conducted to elucidate its structure. The backbone of GCPB-2 was composed of (1 → 4)-linked-β-d-xylopyranose residues which branched at O-3. The two branches consisted of (1 → 3)-linked-β-l-arabinopyranose terminated with β-d-xylopyranose residues, and (1 → 4)-linked-β-l-arabinopyranose terminated with β-d-arabinopyranose residues. In the in vitro antioxidant assay, GCPB-2 was found to possess 1-diphenyl-2-picryl-hydrazyl (DPPH) radical-scavenging activity with an EC50 value of 0.379 μM. The findings of this study indicated that GCPB-2 possesses the hydroxyl radical-scavenging activity, which provided an experimental evidence to support the G. capense as functional foods in some Asian countries. To understand better the bioactivity of GCPB-2, the antioxidant activity should be further investigated to find out its mechanism in future work. © 2015 Elsevier Ltd. All rights reserved.