The regulation of nitrogenase. biosynthesis in the heterocystous blue-green alga, Anabaena cylindrica was studied in vivo. The action of ammonia on nitrogenase activity during heterocyst induction and in fully differentiated cultures was compared with that of selective inhibitors of transcription and translation. The process of heterocyst differentiation is known to become refractory to inhibition by ammonia at some intermediate stage. We now report that nitrogenase induction is also inhibited only in the early stages of heterocyst development. Later in the differentiation process, nitrogenase activity continued to increase in the presence of ammonia. The addition of ammonia to logarithmically growing cultures had little effect on nitrogenase activity on a volume basis; however, no new heterocysts were formed and specific activity declined as the cultures grew. Nitrogenase under these conditions is not stable since inhibition of protein synthesis resulted in rapid loss of enzyme activity. Thus nitrogenase biosynthesis does not appear to be inhibited in heterocysts. Dramatic losses of nitrogenase activity were found after prolonged ammonia treatment of linear phase cultures. H2 stimulated nitrogenase activity to nearly control levels and sensitivity to DCMU (in the presence of O2) increased while dark activities were lost. These findings suggest indirect effects of ammonia or its metabolites (e.g. glutamine) on heterocyst differentiation, reductant supply, and oxygen protection, rather than a direct effect on nitrogenase biosynthesis.