Fusarium pseudograminearum is a pathogenic fungus in wheat newly found in China. The purpose of this study was to disclose the responses of genes involved in the hormone signals pathway to F.pseudograminearum infection. Wheat cultivar Zhoumai 24 wasinfected by the wild-type strain WZ2-8A, and the seedling samples at fiveand fifteendays after inoculation (DAI)were subject to transcriptome analysis by RNA-seqmethod. Theselected differentially expressed genes were subsequently validated by qRT-PCR assay. The infection ofF. pseudograminearum had a negative impact on wheat growth with significantly decreased root length, seedling height, and fresh weights of root and shoot. Atotal of 29 genes expressed differentially in the signal transduction pathways of auxin, cytokinin (CTK) and abscisic acid (ABA). At 5 DAI, 11 genes were expressed differentially compared with the control group (without WZ2-8A inoculation), in whichtwo and nine genes were up- and down-regulated, respectively. At 15 DAI, 25 genes were expressed differentially,including eightup-regulated and seventeendown-regulated genes. In the auxin signaling pathway, auxin input transporter AUX1 was differentially expressed, influencing polar transport of auxin and disturbing cell elongation of wheat roots.In the CTK signaling pathway, the up-regulating role of B-ARR suggests that it couldfacilitate CTK signal transduction to inhibit cellular division,resulting in weaker wheat growth along with the interaction of the auxin signaling pathway. In the ABA signaling pathway, ABA receptor PYR/PYL was down-regulated, while the negative regulator PP2C was up-regulated. ABA plays a negative role in regulating host resistance to fungi and bacteria and its transduction has the antagonistic action against the jasmine acid (JA) / ethylene (ET) pathway, i.e., the repression of ABA signaling pathway might result in the opening ofJA/ET pathway. These results of transcriptome analysis were generally validated bythe qRT-PCR evidence, indicating that inhibition of ABA signal transduction after F. pseudograminearum infection might be the physiological basis of moderate resistance to the fungus in Zhoumai 24.