Control of sulfate reduction by adding molybdate was investigated to enhance the methane production under batch and continuous operation in the anaerobic digestion of a sulfate-rich lysine wastewater. In phase 1 of the continuous operation, four anaerobic filters were fed with the lysine wastewater and then added with molybdate at 1,3,5 and 10 mM just after methane producing bacteria (MPB) were completely inhited by H2S produced by sulfate reducing bacteria (SRB). In phase 2, three anaerobic filters were operated with continuous or intermittent addition of 3 mM molybdate from the beginning of operation, including one with no molybdate as a control. Batch experiments revealed that the sulfate reduction was strongly inhibited and finally ceased by adding 3 mM or more of molybdate, resulting in great enhancement of the methane production. In phase 1 of the continuous experiments, all reactors showed the cessation of the methane production when the content of H2S reached 9–10 % in biogas, but the MPB activity was gradually recovered after initiating the molybdate addition at 3 or 5 mM. The 10 mM dosage of molybdate, however, had an inhibiting effect to MPB as well as SRB, resulting in the accumulation of acetate within the reactor. In phase 2, the control reactor continued to decrease the methane production, and a methane conversion rate was only 3 % in the control, while 35 and 10 % in continuously-added and intermittently-added reactors, respectively. Thus, it was confirmed that the MPB activity was greatly enhanced under control of the SRB activity by the continuous addition of molybdate. Comparing phase 2 with phase 1, addition from the start-up of the process is considered more effective than addition after the methane production dropped in the control of the sulfate reduction by molybdate.