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Ginger (<i>Zingiber officinale</i> Roscoe) is an important horticultural crop, valued for its culinary and medicinal properties. Fusarium yellows of ginger, caused by <i>Fusarium oxysporum</i> f. sp. <i>zingiberi</i> (<i>Foz</i>), is a devastating disease that has significantly reduced the quality and crop yield of ginger worldwide. The compatible interaction between ginger and <i>Foz</i> leading to susceptibility is dissected here. The pathogenicity of two <i>Foz</i> isolates on ginger was confirmed by their ability to colonise ginger and in turn induce both internal and external plant symptoms typical of Fusarium yellows. To shed light on <i>Foz</i> susceptibility at the molecular level, a set of defense-responsive genes was analysed for expression in the roots of ginger cultivars challenged with <i>Foz</i>. These include nucleotide-binding site (NBS) type of resistant (<i>R</i>) genes with a functional role in pathogen recognition, transcription factors associated with systemic acquired resistance, and enzymes involved in terpenoid biosynthesis and cell wall modifications. Among three <i>R</i> genes, the transcripts of <i>ZoNBS1</i> and <i>ZoNBS3</i> were rapidly induced by <i>Foz</i> at the onset of infection, and the expression magnitude was cultivar-dependent. These expression characteristics extend to the other genes. This study is the first step in understanding the mechanisms of compatible host–pathogen interactions in ginger.