Due to the huge quantity and diverse nature of their metabolic pathways, fungi have great potential to be used for the production of different biofuels such as bioethanol, biobutanol, and biodiesel. This book presents recent advances, as well as challenges and promises, of fungal applications in biofuel production, subsequently discussing plant pathogenic fungi for bioethanol and biodiesel production, including their mechanisms of action. Additionally, this book reviews biofuel production using plant endophytic fungi, wood-rotting fungi, fungal biocontrol agents, and gut fungi, and it investigates highly efficient fungi for biofuel production and process design in fungal-based biofuel production systems. Finally, life cycle assessment of fungal-based biofuel production systems are discussed in this volume.