Salmonella enterica serovar Typhi z66-positive strain contains an fljBA-like operon on a linear plasmid and the fliC gene on the chromosome encoding d or j antigen. The fljB-like gene has been identified as the gene encoding z66 antigen. To investigate the function of the fljA-like gene in S. enterica serovar Typhi, a z66-positive wild-type strain GIFU10007 and its phase variation j positive strain 007j+ were used in the present study. After deletion of the fljA-like gene, the wild-type strain that only expressed FljB:z66 could express both FliC:j and FljB:z66 at the same time. A recombinant plasmid, pBADfljA, containing the fljA-like gene was prepared. SDS-PAGE and western blot analysis of secreted proteins showed that when the strain 007j+ was transformed by the recombinant plasmid, pBADfljA, the expression of FliC:j was inhibited. The fliC::lacZ fusion of the strain 007j+ was constructed. Beta-Galactosidase activity was decreased approximately 100-fold after harboring the plasmid pBADfljA in the fliC::lacZ mutant strain. However, the fliC mRNA level investigated by RT-PCR was decreased only approximately seven-fold in the strain 007j+ after harboring the plasmid pBADfljA. These results demonstrated that thefljA-like gene on a linear plasmid of S. enterica serovar Typhi is a fljA gene, the repressor of fliC gene, and the inhibition by FljA is likely at the post-transcriptional level.