Methane fermentation is an effective way to treat wet organic wastes. Since methane fermentation is a multistage process, intermediates are likely to accumulate and cause fermentation inhibition. Two phase methane fermentation process enables further accurate control of the environmental conditions to suit each reaction and this will prevent fermentation inhibition. Hydrogen-methane two phase fermentation process can produce both H2 and CH4, and increase total energy quantity. Partial recirculation of methane fermentation sludge will act as inoculum compensation and pH control for the hydrogen fermentation process because the sludge includes hydrogen producing bacteria. Since methane fermentation sludge includes also hydrogen consuming microbes such as methanogenic bacteria and those that compete with hydrogen producing bacteria for substrate, making hydrogen producing bacteria dominant is necessary for a fine hydrogen- methane process. Heat treatment to the methane fermentation sludge has been used for effectively making the hydrogen fermentation bacteria dominant. This research aimed to develop a new treatment technology for effectively dominating the hydrogen producing bacteria. Hot compressed water (HCW) treatment was employed as a new treatment technology and was compared with heat treatment. Hydrogen fermentation was performed by using treated seed sludge and the effectiveness of the treatment was evaluated. Mesophilic methane fermentation sludge from food waste was used as seed sludge. Heat treatment was operated by a water bath at 95 °C for 2 h. HCW treatment was operated at 150 °C for 40 min as retention time under three different pressures 0.5, 2.5 and 4.5 MPa. Hydrogen fermentation was performed with a 100 ml batch reactor adding 0.375 g glucose as substrate in an incubator at 37 °C for 150h. Gas generation and composition were measured every 6 h with GC. The organic acid and glucose concentration was measured with HPLC after fermentation. Microbial community structure was analyzed with a next-generation DNA sequencer on the hydrogen fermentation sludge. HCW treatment at 0.5 MPa was effective and high hydrogen yield over 1.5 mol- H2/mol-glucose was obtained in two of three replicates, which was 4 times higher than non-treatment, and 3 times higher than heat treatment. Microbial community structure analysis showed that HCW treatment at 0.5 MPa was more effective than heat treatment for eliminating methanogenic bacteria and dominating Clostridium.