Water Hyacinth (WH) remains an intractable challenge worldwide hindering the aquatic ecosystems but a potential lignocellulosic biomass for the generation of renewable biogas through Anaerobic Digestion (AD). Here, autoclave pretreatment at 121 °C for 30 min was utilized to pretreat WH in order to enhance its solubilization. Cow Dung (CD), as a source of microorganisms, was mixed with the pretreated WH (1:1 w/w dry basis) followed by mixing with water to form slurry and digested for 50 days to explore its prospective biomethanation. The untreated WH exhibited its highest yield of methane (113 ± 11 mL CH 4 /g VS) on the 35 th day whereas for the pretreated WH slurry, this yield was increased to 150 ± 9 mL CH 4 /g VS on the 21 st day. Clearly, the autoclave pretreated WH exhibited enhanced CH 4 -containing biogas production as the highest methane yield obtained in a short time. The microbial communities were tested by using VIT® gene probe. The total bacterial communities were quantified by qPCR targeting 16S rRNA genes using a LIVE/DEAD test. The functional gene, mcr A, was used as a target for detecting the most abundant methanogenic Archaea . The results revealed that six bacterial phyla were dominant. Of these, Proteobacteria , Bacteroidetes and Chloroflexi were the most abundant phyla (86.1 ± 5.2%). The qPCR showed viable and total cell counts of 2.45E + 09 and 5.11E + 09 cells/mL, respectively. The mcr A gene qPCR decreased by approximately 10.7% viable cells overall after the biomethanation. Using specific gene probes, the methanogenic Archaea were identified as members of the genus Methanosarcina .