This study investigated the effect of saponins gypenoside (gynosaponins) on methane production and microbe numbers in a co-culture of a fungus, Piromyces sp. F1, and a methanogen, Methanobrevibacter sp.. Two co-culture systems were used: with methanogen (co-culture I) and without methanogen (co-culture II; methanogen growth inhibited by chloramphenicol). Each co-culture system was treated with 0, 50, 100 or 200 mg gynosaponins/l culture medium. Gas production, methane concentration and volatile fatty acid concentration (VFA) were measured for each treatment group. The numbers of anaerobic fungi and methanogen were quantified by real time PCR. The results showed that, compared with the control, gynosaponin significantly reduced the gas production, methane concentration, methane to TVFA ratio (total volatile fatty acid), TVFA concentration, number of fungi (except for 50 mg dose of gynosaponin in co-culture I) and number of methanogens. Methane was not detected in co-culture II. The individual VFAs proportion of TVFA were not affected by gynosaponins in either of the co-cultures. The pH was higher in both co-cultures than that of the control (P<0.01). These data suggest that gynosaponins has the potential for being used as feed additive to modulate the ruminal fermentation, inhibit the methanogen growth and reduce methane production.