The Bordetella pertussis response regulator, BvgA acts directly as a transcriptional activator at the locus encoding petussis toxin (ptx) and that encoding fialmentous hemagglutinin (fha). Previous studies have demonstrated that these two loci are differentially regulated by BvgA. As an initial step in gaining insight into how BvgA may distinguish between fha and ptx, we have initiated DNA binding and in vitro transcription analyses to examine the activities of BvgA and RNA polymerase (RNAP) purified from both B. pertussis and E. coli at the fha promoter. We discovered that unphosphorylated BvgA binds to a single upstream region, whereas BvgA phosphorylated in vitro binds both this region and another further downstream that extends to the 35 nucleotide. In the absence of BvgA, RNAP binds a region farther upstream than expected. However, occupation of both sites by BvgA phosphate repositions RNAP to the site used in vivo. The binding of RNA polymerase and BvgA phosphate is cooperative and this enhancement correlates with the in vitro transcription activity at the fhapromoter. We observed that polymerases carrying either a deletion of the Cterminal domain of the asubunit, or the substitution of alanine for two critical residues within this domain were severely impaired in their ability to mediate BvgAactivated transcription at fha.