Increased energy consumption coupled with the ongoing climate change are urging us to develop more sustainable energy alternatives, including biofuels produced from renewable biomass. Our heavy reliance on fossil-derived fuels has not only gained intense public attention in recent years, but has also prompted us to intensively study the production of sustainable biofuels from renewable energy sources via microbial fermentation.  Owing to the recent advances and availability of state-of-the-art molecular tools, our knowledge about anaerobic microorganisms and their direct and indirect contributions in the production of different biofuels have increased tremendously. Anaerobic microorganisms are mainly utilized for commercial production of biofuels such as; biogas and fuel alcohols from renewable organic matter, while photosynthetic microorganisms convert inorganic carbon and water to potential fuels (e.g. fuel alcohols) and fuel precursors (e.g. biomass, starch, lipids). Although metabolically engineered microorganisms, programmed to redirect renewable carbon sources into desired fuel products, are contemplated as best choices to obtain high volumetric productivity and yield, however, native populations of anaerobic microorganisms are still considered the primary choice for the production of biogas and bioethanol. These anaerobic microorganisms responsible for different degradation pathways and their functions in anaerobic digesters are continuously being updated.  In this review, we discuss the essential role of anaerobic microbes in biogas and bioethanol production via consolidated anaerobic process. Additionally, key enzymatic reactions and microbiota involved in the degradation steps and in the production pathways are specifically highlighted. We also discussed the challenges that still exist for biofuel production from native populations of anaerobic microorganisms and their possible solutions.