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<i>Gastrodia elata</i> is a valuable traditional Chinese medicinal plant. However, <i>G. elata</i> crops are affected by major diseases, such as brown rot. Previous studies have shown that brown rot is caused by <i>Fusarium oxysporum</i> and <i>F. solani</i>. To further understand the disease, we studied the biological and genome characteristics of these pathogenic fungi. Here, we found that the optimum growth temperature and pH of <i>F. oxysporum</i> (strain QK8) and <i>F. solani</i> (strain SX13) were 28 °C and pH 7, and 30 °C and pH 9, respectively. An indoor virulence test showed that oxime tebuconazole, tebuconazole, and tetramycin had significant bacteriostatic effects on the two <i>Fusarium</i> species. The genomes of QK8 and SX13 were assembled, and it was found that there was a certain gap in the size of the two fungi. The size of strain QK8 was 51,204,719 bp and that of strain SX13 was 55,171,989 bp. Afterwards, through phylogenetic analysis, it was found that strain QK8 was closely related to <i>F. oxysporum</i>, while strain SX13 was closely related to <i>F. solani</i>. Compared with the published whole-genome data for these two <i>Fusarium</i> strains, the genome information obtained here is more complete; the assembly and splicing reach the chromosome level. The biological characteristics and genomic information we provide here lay the foundation for further research on <i>G. elata</i> brown rot.