In order to efficiently utilize the biomass waste of algae bloom in Taihu Lake, China and improve energy conversion efficiency, a three-stage process comprising dark hydrogen fermentation with acid-domesticated hydrogenogens, photohydrogen fermentation, and methanogenesis was undertaken. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses showed that algal cells pretreated by microwave heating with diluted acid were degraded into smaller fragments (<5 mu m) than those pretreated by steam heating with diluted acid. The microwave pretreatment of algae resulted in higher saccharification efficiency. The domesticated hydrogenogens in presence of acids improved the dark hydrogen production from microwave-pretreated algae biomass and led to a total combined dark and photofermentation hydrogen yield of 283.4 mL/g-total volatile solid (TVS). The energy conversion efficiency of steam-pretreated algae biomass remarkably increased to 47.0% by cogenerating 256.7mL/g-TVS hydrogen and 253.5 mL/g-TVS methane in the three-stage process: dark-fermentation, photofermentation, and methanogenesis. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.