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<i>Fusarium</i> wilt disease is one of the major diseases causing a decline in watermelon yield and quality. Researches have informed that phytohormones play essential roles in regulating plants growth, development, and stress defendants. However, the molecular mechanism of salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in resistance to watermelon <i>Fusarium</i> wilt remains unknown. In this experiment, we established the SA, JA, and ABA determination system in watermelon roots, and analyzed their roles in against watermelon <i>Fusarium</i> wilt compared to the resistant and susceptible varieties using transcriptome sequencing and RT-qPCR. Our results revealed that the up-regulated expression of <i>Cla97C09G174770</i>, <i>Cla97C05G089520</i>, <i>Cla97C05G081210</i>, <i>Cla97C04G071000</i>, and <i>Cla97C10G198890</i> genes in resistant variety were key factors against (<i>Fusarium oxysporum f. sp. Niveum</i>) FON infection at 7 dpi. Additionally, there might be crosstalk between SA, JA, and ABA, caused by those differentially expressed (non-pathogen-related) NPRs, (Jasmonate-resistant) JAR, and (Pyrabactin resistance 1-like) PYLs genes, to trigger the plant immune system against FON infection. Overall, our results provide a theoretical basis for watermelon resistance breeding, in which phytohormones participate.