In Anabaena, the pipX gene is induced in the cells differentiating into heterocysts, being the PipX factor required for full expression of late heterocyst‐specific genes. Here we show that PipX has a positive effect on in vitro binding of the transcription factor NtcA to DNA, as well as on transcript production, in different NtcA‐dependent promoters. We found that the cox3 operon, encoding a heterocyst‐specific terminal respiratory oxidase, is expressed from three nitrogen‐regulated promoters to which NtcA binds. At the three sites, NtcA binding is potentiated by PipX. Thus, PipX has a direct effect on gene expression influencing the activity of NtcA.