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<i>Vernicia fordii</i> (tung oil tree) is famous in the world for its production of tung oil. Unfortunately, it was infected by the soil-borne fungus <i>Fusarium oxysporum f.</i> sp. <i>fordii</i> 1 (<i>Fof</i>-1) and suffered serious wilt disease. Conversely, its sister species <i>V. montana</i> is highly resistant to <i>Fof</i>-1. The MYB (v-myb myeloblastosis viral oncogene homolog) transcription factors were activated during the pathogen <i>Fof</i>-1 infection according to our previous comparative transcriptomic results. Depending on whether the sequence has a complete MYB-DNA-binding domain, a total of 75 <i>VfMYB</i> and 77 <i>VmMYB</i> genes were identified in susceptible <i>V. fordii</i> and resistant <i>V. montana</i>, respectively. In addition, we detected 49 pairs of one-to-one orthologous <i>Vf/VmMYB</i> genes with the reciprocal-best BLAST-hits (RBH)method. In order to investigate the expression modes and the internal network of MYB transcription factors in the two species responding to <i>Fusarium</i> wilt disease, the expressions of <i>Vf/VmMYBs</i> were then investigated and we found that most orthologous <i>Vf/VmMYB</i> genes exhibited similar expression patterns during the <i>Fof</i>-1 infection. However, four pairs of <i>Vf/VmMYB</i> genes, annotated as unknown proteins and mediator of root architecture, demonstrated absolute opposite expression patterns in the two <i>Vernicia</i> species responding to <i>Fof</i>-1. The interaction network of <i>VmMYB</i> genes were further constructed using weighted gene co-expression network analysis (WGCNA) method and four hub genes showing extremely high interaction with the other 1157 genes were identified. RT-qPCR result verified the opposite expression pattern of the hub gene <i>VmMYB011</i> and <i>VmMYB041</i> in two <i>Vernicia</i> species. In summary, co-expression network of the <i>Vf/VmMYBs</i> and significantly opposite related pairs of genes in resistant and susceptible <i>Vernicia</i> species provided knowledge for understanding the molecular basis of <i>Vernicia</i> responding to <i>Fusarium</i> wilt disease.