In the filamentous cyanobacterium Calothrix PCC 7504, which fixes N-2 aerobically, the modification state of the regulatory P-II protein (GlnB) was shown to depend on nitrogen and carbon availability, as observed in the unicellular non-fixing strain Synechococcus PCC 7942. However, the conditions for modifications, the time dependence of the process and the electrophoretic behavior of the native P-II isoforms differed somewhat between the two strains. In another strain, Calothrix PCC 7601, which has lost the capability to fix N-2, P-II was modified only if ammonia plus an inhibitor of glutamine synthetase were present. It is proposed that: (i) the behavior of the P-II proteins depends upon the physiological properties of the strains; and (ii) the modification system of P-II per se may differ between the two cyanobacterial genera.