This datasets collection includes: - For Scedosporium aurantiacum MUT6114 and S. minutisporum MUT6113: fasta files with assembled genome sequences, and gff files with coordinates of both genes and putative TEs insertions. All these files were generated by the authors of this study. - For S. apiospermum IHEM 14462 and Lomentospora prolificans JHH-5317: gff files containing putative TEs insertions only, since the genomic sequences and the gene models were produced by other authors and deposited in the NCBI database under accession numbers GCF_000732125.1 and GCA_002276285.1, respectively. - For S. apiospermum HDO1, S. aurantiacum WM09.24, S. boydii IHEM23826, S. dehoogii 120008799-01-4, Scedosporium sp. IMV00882 and Scopulariopsis brevicaulis LF580: gff files with coordinates of both genes and putative TEs insertions, since the genomic sequences were produced by other authors and deposited in the NCBI database under accession numbers GCA_002158515.1, GCA_000812075.1, GCA_002221725.1, GCA_002812735.1, GCA_001931805.1 and GCA_017657125.1, respectively.