Biofuels and bioenergy not only benefit independence of energy supply, but also mitigate CO2 emissions. This special issue includes review reports and research articles involving various biofuels and bioenergy products and systems such as fuel ethanol, biodiesel, biogas, biohydrogen, microbial fuel cells and microbial electrolysis cells. Both fundamental research and technology development are highlighted. And in the meantime, challenges for large scale production and application of biofuels and bioenergy are discussed. Taking advantages of modern biotechnology advances, solutions to address these challenges are envisioned.