Bioinformatic approaches are employed to study NtcA and NtcB regulons, particularly, the factors binding sites, in cyanobacteria and chloroplasts of Rhodophyta. We predict 477 candidate NtcA sites in cyanobacteria (441 in species with no experimental data) and 44 candidate NtcB sites (40 in species with no experimental data). The sites are found upstream of 24 orthologous gene families (84 families studied in total) in 51 species. The consensus of NtcA binding sites is a 20 b.p.-long degenerate palindrome with the conserved core GTA-8N-TAC. The NtcB sites consensus is TGCA-5N-TGCA. We infer the evolution of NtcA- and NtcB-regulons. Particularly, the NtcA factor is shown to repress genes gifA, gifB and activate apcF and som in many cyanobacteria. A mechanism of transcription regulation of the glnB gene as a part of NtcA-regulon is proposed in Rhodophyta.