Microorganisms remain the powerhouse in the different processes of anaerobic digestion (AD). These organisms in a synergistic approach convert organic matters to biogas and other useful products. Over time, the study of these microbes involved in AD has been a challenge. This is because of the high limitations of the culturebased techniques in the isolation of microorganisms. The advent of molecular techniques in the study of microbes in AD has become a groundbreaking achievement. Meta-omics give very deep insights not only into the diversity of microbiota present but into the microbiome and pathways involved. More studies are required using molecular techniques to unlock more information about these tiny but powerful living machines that help in balancing and maintaining both the aerobic and anaerobic ecosystems.