Microwave-heated alkali pretreatment (MAP) was investigated to improve enzymatic digestibility and H-2/CH4 production from water hyacinth. SEM revealed that MAP deconstructed the lignocellulose matrix and swelled the surfaces of water hyacinth. XRD indicated that MAP decreased the crystallinity index from 16.0 to 13.0 because of cellulose amorphisation. FTIR indicated that MAP effectively destroyed the lignin structure and disrupted the crystalline cellulose to reduce crystallinity. The reducing sugar yield of 0.296 g/gTVS was achieved at optimal hydrolysis conditions (microwave temperature = 190 degrees C, time = 10 min, and cellulase dosage = 5 wt%). The sequentially fermentative hydrogen and methane yields from water hyacinth with MAP and enzymatic hydrolysis were increased to 63.9 and 172.5 mL/gTVS, respectively. The energy conversion efficiency (40.0%) in the two-stage hydrogen and methane cogeneration was lower than that (49.5%) in the one-stage methane production (237.4 mL/gTVS) from water hyacinth with MAP and enzymatic hydrolysis. (c) 2015 Elsevier Ltd. All rights reserved.