The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome dysbiosis in different stages of anaerobic digestion, we analyzed 16 samples dividing into four groups (Group-I = 2; Group-II = 5; Group-III = 5 and Group-IV = 4) through whole metagenome sequencing (WMS). The physicochemical analysis revealed that highest CH 4 production (74.1%, on Day 35 of digestion) was associated with decreased amount of non-metal (phosphorus and sulfur) and heavy metals (chromium, lead and nickel). The WMS generated 380.04 million reads mapped to ~ 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. The PS analysis detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively which were represented by Firmicutes , Bacteroidetes , Proteobacteria , Actinobacteria , Spirochaetes and Fibrobacteres (> 93.0% of the total abundances). The archaeal fraction of the AD microbiomes was represented by 343 strains, of which 95.90% strains shared across these metagenomes. The indicator species analysis showed that Methanosarcina vacuolate , Dehalococcoides mccartyi , Methanosarcina sp. Kolksee and Methanosarcina barkeri were the highly specific for energy production in Group-III and Group-IV. However, most of the indicator phylotypes displayed reduced abundance in the initial stage of biogas production (Group-I and Group-II) compared to their increased relative abundances in Group-IV (Day 35). The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla were associated with highest level (74.1%) of energy production (Group-IV). In addition to taxonomic dysbiosis, top CH 4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, MT1-MMP pericellular network, acetyl-CoA production, motility and chemotaxis. This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.