The animal intestine provides a competitive environment for the microbiota. Successful colonization by pathogens requires sensing chemical signals to regulate the expression of virulence genes. Some bacteria rely on a two-component chemical signal transduction system, named FusKR, to regulate virulence genes expression by intestinal fucose. Here we construct the fucP gene deletion strain prove FucP regulation of the T3SS in E. tarda. The result showed that the mutant strain had down-regulated significantly the gene expression of FusKR and T3SS compared to the wild-type strain (P < 0.05). This mutant strain significantly increased LD50 in zebrafish compared to the wild-type strain (P < 0.05), and significantly decreased penetration and motility in mucin than the wild-type strain (P < 0.05). Meanwhile, tilapia infected with mutant strain show significantly reduced E. tarda adherence and colonization than those infected with the wild-type strain (P < 0.05). Fish infected with EIB202 and ΔfucP showed significantly higher (P < 0.05) gene expression of IL-1β, TNF-α, IFN-γ, TGF-β and HSP-70 in head kidney than fish treated with PBS in the whole observed period; however CPP-3 did not show significant differences (P > 0.05) in all groups. Fish infected with EIB202 showed significantly higher (P < 0.05) gene expression of TGF-β in head kidney than fish treated with ΔfucP in the whole observed period; however other cytokines did not show significant differences (P > 0.05) in the whole observed period. In addition, Fish infected with EIB202 showed significantly higher (P < 0.05) gene expression of IL-1β, TNF-α and TGF-β in spleen than fish treated with ΔfucP in the whole observed period, however IFN-γ, CPP-3, and HSP-70 did not show significant differences (P > 0.05) in the whole observed period. Although the gene expression of cytokines was induced similarly by both strains, all results indicate that the fucP gene deletion down-regulates the key gene expression of FucKR and T3SS, reduces the pathogenicity of E. tarda in fish, particularly decreases inducing the gene expression of TGF-β in the head kidney and IL-1β, TNF-α and TGF-β in the spleen.