Plant-associated microbes are ubiquitous organisms living in a range of interactions with their host. Involving two organisms, research and applications of plant microbes are challenging and often require specific skills. This book guides the reader in the word of plant-associated fungi, giving both theoretical and practical insight on the potential of this interaction in biotechnology. Detailed instructions and step-by-step protocols are described for isolation, identification, localization and community analysis of fungi, studies on their bioactivity, molecular plant-fungal interactions, and development of fungi as tools for biotechnology.