Scedosporium aurantiacum is an emerging pathogen of humans and animals. It is commonly present in urban environments. Animal studies, using the Galleria mellonella model, have revealed virulence differences among strains. To establish a molecular basis for future studies to understand the origin of those differences, we have sequenced and assembled for the first time the genome of S. auarantiacum strain WM 09.24 using different genome assemblers. To project the genome annotation and develop gene models we performed whole-genome alignment with the next closest species for which an annotated genome was publically available, Trichoderma virens. However, this species is still so distant that only approximately 30 % of the two genomes could be aligned through whole-genome alignment. Therefore, neither direct-gene projection nor BLAST searches could be applied in order to annotate the S. aurantiacum genome. To overcome this problem we performed RNA-sequencing of strain WM 09.24 under different growth conditions (to maximise the number of transcribed genes), and used the JAMg pipeline to annotate the genome. The annotated genome of strain WM 09.24 was then used to annotate three additional S. aurantiacum strains with varying virulence to enable a whole-genome comparison to identify genes or genetic signatures that are associated with virulence.