The increase energy demand by the due to the growth of human population could cause decreasing fossil fuel energy. In near future energy demand will increase rapidly in the future. All those problems require each country to produce and to use renewal energy. Biogas is one of the renewable energy sources that can be used as the alternative energy. This is a kind of methane gas which is formed of various organic waste biomasses such as tofu waste. The aim of this research was to study the dynamic structure of methanogens community in the anaerobic digestion process by T-RFLP method. Sample was taken from anaerobic biodigester on day: 0, 5, 10, 15, and 20 to measure the pH, temperature, CH4, and molecular analysis. The dynamic of methanogens community during anaerobic digestion was observed by the TRFLP (Terminal Restriction Fragment Length Polymorphism) technique. The restriction enzyme used in that method was Alu1. The Shannon-Wiener (H’) index was used to analyze the community diversity. The research obtained by three filotipe detected by TRFLP , namely the Euryarchaeota on fragment size 62 bp, Archaea in the size of the fragment 136, and Methanosphaerula palustrispada in fragment size 167 bp. The Methanosphaerula palustris was dominating community member from beginning until the end of the fermentation process. The result of pH measurements ranged from 7 to 8. The highest CH4 production was on day 5 equal to 1092.6 ppm. The temperatures range from 30-310C.