The bulk of livestock excreta is utilized as compost across the country, but there is also a considerable amount composted by the weather. Environmental concerns such as groundwater pollution and offensive odors are thus surfacing in regions crowded with dairy farms. We are now conducting research on agricultural and livestock waste treatment, along with a series of case studies on anaerobic digestion treatment processes that is expected to develop into a full-fledged study. Based on the research findings, we have developed a membrane separation methane fermentation system that is designed to denitrify supernatant liquor associated with methane fermentation. Experiments were conducted on bench-scale methane fermentation to review this system, and on a methane fermentation system with a membrane separation process, the results of which are shown in this report. The system is intended to increase the concentration of bacteria in methane fermentation fluid, and to obtain clear filtered fluid.