Microorganisms play a significant role in anaerobic digestion of organic matter in order to add up the chemical substances in the ongoing biochemical process. The microbes are responsible for the efficient breakdown of complex organic molecules through a series of biochemical reactions for methane production. In the present study inoculums were collected from three different sources – a sewage sludge wastewater treatment plant (SS), cow dung (CD), and an anaerobic reactor treating inoculum from organic matter (IOM) – to evaluate their potential for anaerobic digestion of agricultural residues (AR) and fruit vegetable waste (FVW) at mesophilic temperature (35ºC). The higher biogas production of 507 l/gVS was achieved for a mixture of inoculums (SS+CD+IOM) in reactor 4 (R4), and biogas characterization by gas chromatography (GC) reveals 67.7% of the methane content. The morphological, biochemical, and molecular techniques were used to identify the microbial flora present in the high-yield reactor. The abundance of Bacillus, clostridium, and Enterobacter spp were observed along with Methanomicrobia and Methanosarcina. To get a high methane yield from organic waste it is necessary to maintain the equilibrium and availability of efficient microbial communities like firmicutous, hydrogenotrophic, and acitoclatic methanogens.