In Bradyrhizobium japonicum the napEDABC, nirK, norCBQD and nosRZDYFLX genes, which encode reductases for nitrate, nitrite, nitric oxide and nitrous oxide, respectively, are required for denitrification. Microaerobic induction of these genes depends on fixLJ and fixK2, whose products form the FixLJ-FixK2 regulatory cascade. In B. japonicum, a second oxygen-responsive regulatory cascade mediated by the nitrogen fixation regulatory protein, NifA, has been described. In this study, we show that disruption of nifA caused a growth defect in B. japonicum cells, when grown under denitrifying conditions, and decreased activity of periplasmic nitrate and nitrite reductase enzymes was also observed. Furthermore, expression of napE-lacZ, nirK-lacZ or norC-lacZ transcriptional fusions, as well as levels of nirK transcripts were significantly reduced in the nifA mutant after incubation under nitrate-respiring conditions. Haem c staining analyses revealed that NifA is required for full synthesis of the NapC and NorC proteins, which are required for denitrification. A B. japonicum rpoN1/2 mutant, lacking both copies of the gene encoding the alternative sigma factor sigma54, was able to grow anaerobically with nitrate as terminal electron acceptor and showed wild-type levels of nitrate and nitrite reductase activities. We propose that the nitrogen fixation regulatory protein, NifA, is involved in the maximal expression of the denitrification genes in B. japonicum. This influence is independent of sigma54.