The thermodynamic comparison in dark fermentation between amino acids and reducing sugars released from Nannochloropsis oceanica biomass are investigated for the first time. The total utilisation efficiencies of amino acids and reducing sugars are both about 95% in dark fermentation. But the consumption time of most amino acids is about 2 times as long as that of most reducing sugars in dark fermentation. A three-stage method comprising dark fermentation, photofermentation and methanogenesis is proposed to improve hydrogen and energy yields from N. oceanica biomass. Overall, the maximum hydrogen yield of 183.9 ml/g-total volatile solids (TVS) and the methane yield of 161.3 ml/g-TVS are achieved from N. oceanica biomass through the three-stage method. The total energy yield of hydrogen and methane from microalgae biomass through the three-stage method is 1.7 and 13 times higher than those through the two-stage (dark fermentation and methanogenesis) and single-stage (methanogenesis) methods, respectively. (c) 2013 Elsevier Ltd. All rights reserved.