HetR plays a key role in regulation of heterocyst differentiation. When the Cys-48 residue of the HetR from Anabaena sp. PCC 7120 was replaced with an Ala residue, the mutant HetR (HetR(C48A)) could not dimerize, indicating that HetR forms a homodimer through a disulfide bond. The Anabaena strain C48, containing the hetRc48a gene, could not produce HetR homodimer and failed to form heterocyst. We show that HetR is a DNA-binding protein and that its homodimerization is required for the DNA binding. HetR binds the promoter regions of hetR, hepA, and patS, suggesting a direct control of the expression of these genes by HetR. We present evidence that shows that the up-regulation of patS and hetR depends on DNA binding by HetR dimer. The pentapeptide RGSGR, which is present at the C terminus of PatS and blocks heterocyst formation, inhibits the DNA binding of HetR and prevents hetR up-regulation.