The objective of this study was to investigate the cytotoxicity of the ethanolic extract of mycelia from Ganoderma lucidum (EMG) cultivated in a medium containing leguminous plants Glycine max (L.) Merr. and Astragalus membranaceus on human hepatocellular carcinoma cells (Hep 3B) and to isolate the active components from EMG. The results indicated that EMG induced cytotoxicity in a dose- and time-dependent manner, and the cells treated with EMG for 24, 48, and 72 h had IC(50) values of 156.8, 89.9, and 70.1 microg/mL, respectively. Furthermore, EMG was fractionated into seven fractions (F1-F7). We found that F5 and F6 had higher growth inhibitory effects on Hep 3B cells than the other fractions, and F6 possessed enough amounts (about 2.1 g) to carry out a more detailed study. F6 caused a sub-G1 peak rise and DNA fragmentation in Hep 3B cells and was further separated by high-performance liquid chromatography to obtain two active compounds, 9,11-dehydroergosterol peroxide [9(11)-DHEP] (compound 1) and ergosterol peroxide (EP) (compound 2). The IC(50) values of 9(11)-DHEP and EP based on the cell viability of Hep 3B were 16.7 and 19.4 microg/mL, respectively.