Synthesis of the flagellar apparatus in Escherichia coli is mediated via complex regulatory pathways. A previous study indicated that the protein encoded by the biofilm-dependent modulation (bdm) gene is linked closely with a regulatory pathway for flagellar assembly. However, the specific role of Bdm in flagellar biogenesis remains unknown. Herein, we showed that Bdm interacts with FlgM and inhibits its function as an anti-σ28 factor, which induces the transcription of flagellar late-class genes in E. coli. In addition, we observed that deletion of the yddX gene, a potential Salmonella enterica serovar Typhimurium homolog of bdm, also resulted in downregulation of flagellar late-class genes and in the formation of short flagella, leading to decreased virulence in mice. The expression levels of late-class flagellar genes in yddX-deleted S. Typhimurium cells were restored to those of the wild type when either E. coli bdm or S. Typhimurium yddX was expressed exogenously. These results suggest that Bdm-mediated regulation of flagellar assembly is a conserved regulatory pathway in those members of the Enterobacteriaceae family whose genomes show the existence of homologs of bdm.