Fusarium virguliforme is a soil-borne pathogen that causes sudden death syndrome (SDS) in soybean. SDS is an important disease that causes significant losses in soybean growing areas worldwide. Little is known about the interaction between F. virguliforme and soybean. We have developed a protoplast-based fungal transformation system for F. virguliforme. One of the applications of the transformation system was the production of a green fluorescent protein (GFP)-expressing fungal transformant. The GFP-expressing fungus can be used to study fungal infection processes including fungal penetration, colonization, and spread, especially at the early stages of disease development. Furthermore, in an attempt to increase the genetic resources available to identify and characterize fungal virulence genes involved in the F. virguliforme-soybean system, we generated random insertional mutations in F. virguliforme using restriction enzyme mediated integration.