A fungal endophyte MD89 with obvious antioxidant activities was isolated from pigeon pea and identified as Chaetomium globosum by ITS sequence. Different fractions from MD89 culture were compared and evaluated by total phenol (TP) content, total flavonoid (TFL) content, DPPH radical scavenging, reducing power and lipid peroxidation assays, respectively. Results showed that EtOAc extracts had high content of TP and TFL, and strong antioxidant activities (IC50 value was 6.87, 15.19, 16.78 μg/mL, respectively). Furthermore, the EtOAc extracts were analyzed by LC–MS/MS and a good antioxidant compound, apigenin, was found. The activities of superoxide dismutase (SOD) and glutathione reductase (GR) in HepG2 cells treated with MD89 EtOAc extracts were also determined. It is revealed that EtOAc extracts increased the activities of SOD and GR
in HepG2 cells significantly in a dose-dependent manner. On the basis of those results, we conclude that MD89 represents a valuable natural antioxidant source and may be applicable in health food industry potentially.