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In the present study, <i>Larimichthys crocea</i> and <i>Pseudomonas plecoglossicida</i> were selected as a host-pathogen interaction model for teleosts and prokaryotic pathogens. Five shRNAs were designed and synthesized to silence the <i>fliA</i> gene, all of which resulted in pronounced reductions in <i>fliA</i> mRNA; the mutant strain with the best silencing efficiency of 92.16% was chosen for subsequent analysis. A significant decrease in motility, intracellular survival and escape was observed for the <i>fliA</i>-RNAi strain of <i>P. plecoglossicida</i>, whereby silencing of the <i>fliA</i> gene led to a 30% decrease in mortality and a four-day delay in the onset of infection in <i>L. crocea</i>. Moreover, silencing of <i>P. plecoglossicida fliA</i> resulted in a significant change in both the pathogen and host transcriptome in the spleens of infected <i>L. crocea</i>. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of pathogen transcriptome data showed that silencing <i>fliA</i> resulted in downregulation of 18 flagellum-related genes; KEGG analysis of host transcriptome data revealed that infection with the <i>fliA</i>-RNAi strain caused upregulation of 47 and downregulation of 106 immune-related genes. These pathogen-host interactions might facilitate clearance of <i>P. plecoglossicida</i> by <i>L. crocea</i>, with a significant decrease in <i>fliA</i>-RNAi <i>P. plecoglossicida</i> strain virulence in <i>L. crocea</i>.