Genome sequences of many filamentous fungi are now available and additional genomes are currently being sequenced. One of the next strategic goals is to generate collections of tagged genes in order to establish a link between the several thousands of predicted genes and their function. Transposable elements have been invaluable for the identification and isolation of genes of interest as insertion of a transposon both disrupts and tags a gene. In an effort to exploit active transposons identified in the genome of Fusarium oxysporum as insertional mutagens, a binary system including the tagging element, MITE, and the transposase of a Tc1 element has been established as an efficient tool for gene-tagging in Fusarium graminearum. In this chapter, we provide an overview of the techniques used and highlight some of the critical steps for the application of this tool to other fungal species.