Abstract: Flax wilt is the most destructive fungal disease of flax, hindering cultivation in the main countries producing flax fiber and oil. Its causative agent is the seedborne and soilborne fungus Fusarium oxysporum f. sp. lini. Here we report the assembly of the genomes of three highly pathogenic isolates: F200, F418, and F365. The F418 genome, sequenced on the Illumina and PacBio RS II platforms, was assembled into chromosomes with the MI39 genome assembly as a reference. These results provide firm grounds for comparative genomic studies of plant fungal pathogens, and studies of the evolution of pathogenicity and virulence factors underlying the host–pathogen interactions, thus eventually offering solutions for flax wilt control.