Trehalose was pretreated by microwave heating with dilute acid to improve glucose yield and hydrogen production during dark-fermentation. An optimal glucose yield of 0.95 +/- 0.08 g/g-trehalose was obtained when trehalose was pretreated by microwave heating with 1% dilute H<SUB>2</SUB>SO<SUB>4</SUB> for 25 min at 120 <SUP>o</SUP>C. The hydrolyzed trehalose was inoculated with HPB (hydrogen-producing bacteria) to produce hydrogen during dark-fermentation. The residual solution of dark-fermentation was reused by PSB (photosynthetic bacteria) during photo-fermentation. The residual solution of photo-fermentation was reused by MPB (methane-producing bacteria) during methanogenesis. The maximum yields of hydrogen and methane were 731.3 +/- 33.6 ml/g-trehalose and 116.9 +/- 4.3 ml/g-trehalose. The sequential generation of hydrogen and methane from trehalose remarkably enhanced the energy conversion efficiency from 47.2 +/- 2.2% in hydrogen fermentation to 72.2 +/- 3.1% in combined hydrogen fermentation and methanogenesis.