The genus Fusarium (Ascomycota, Hypocreales, Nectriaceae) includes many economically important plant pathogens, which cause devastating diseases of a wide range of crops and trees. Interestingly, there is increasing evidence that some Fusarium species also live as endophytes and benefit plant growth and stress tolerance. In this work, we sequence the whole genomes of endophytic F. culmorum and F. pseudograminearum, isolated from a coastal dunegrass (Leymus mollis), using long-read SMRT (single-molecule real-time) sequencing technology (PacBio). Their genomes are assembled into four chromosomes and a mitochondrial genome with a total assembly size of 40.05 M and 42.90 M, respectively. This resource should not only facilitate the functional studies designed to better understand what makes the two Fusarium species such successful plant beneficial fungus, but also reveal their genome evolution and adaptation.