This book comprising 13 chapters, is the second of the four books planned for a series on Progress in Mycological Research. The chapters provide an overview of the progress and shifts that have taken place towards the understanding of the Systematics and Evolution of Fungi with the availability of modern tools and techniques. Most major groups of fungi such as the Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota have been attempted to be covered. Advances in morphological and molecular taxonomy of highly toxigenic Fusarium species and understanding the phylogeny of the alternarioid hyphomycetes have also been dealt with in their respective chapters. Methods used in fungal evolutionary biology, their theory, examples and potential applications, and proteomics research for rapid diagnosis to invasive candidiasis have been reviewed in two different chapters. The ways in which molecular biologists and morphosystematists can develop synergy between them has been elaborated in the introductory chapter.