More than 50 genes are required for flagellar formation and function in Salmonella typhimurium. According to the cascade model of flagellar regulon, the flagellar operons are divided into three classes, 1, 2, and 3, with respect to transcriptional hierarchy. FliA is an alternative sigma factor specific for transcription of the class 3 operons, while FlgM is an anti-sigma factor which binds to FliA and prevents its association with RNA polymerase core enzyme. In the present study, we isolated a number of fliA mutants in which the altered FliA proteins become insensitive to inhibition by FlgM. Sequence analysis of their mutation sites revealed that most of them caused the amino acid substitutions in region 4 of the conserved amino acid sequences of sigma factors which lies near the C-terminal end of FliA. Using a set of fliA deletion mutants in a high-expression plasmid, we demonstrated that polypeptides containing the C-terminal portion of FliA could titrate the intracellular FlgM protein resulting in derepression of the class 3 operons. This result indicates that the C-terminal region of FliA contains the FlgM-binding domain. This was confirmed by a chemical cross-linking experiment with FlgM and truncated FliA proteins.