Biofilms are known to play important roles in the disease cycles of bacterial pathogens of plants and animals, where the formations help protect cells from host defense responses and antimicrobial treatments. We have characterized the development of biofilms in Fusarium graminearum in vitro, and are now working towards elucidating the genetics behind the formation. The genetics of filamentous fungal biofilms have not been explored in depth, especially in plant pathogens. Through the use of RNA-sequencing, we have profiled the transcriptome of biofilm formation in F. graminearum over time, which was used to provide candidate genes for phenotypic analysis. The different stages of biofilm development were compared sequentially for differentially expressed transcripts. Stages selected were initial adhesion, initial development of the extracellular polymeric matrix, development of conidia within the biofilm, and mature biofilm formations. Additionally, we have selected a strain of the wild-type fungus which exhibits enhanced adhesion, an important biofilm phenotype. This strain was obtained by only eighteen rounds of selection for adhesive properties, indicating that adhesion is likely to be a property that can adapt quickly to new situations. Understanding the genetics behind the development of F. graminearum biofilms can provide insight into how these structures form and influencing disease development.