The relationship between assimilation of nitrogen and animating activities of glutamine synthetase (GS), NADH-glutamate dehydrogenase (GDH) and NADPH-GDH in ammonium-grown Chlamydomonas pulsatilla Wollen-weber and ammonium- and nitrate-grown Brachiomonas submarina Bohlin and Tetraselmis succica (Kylin) Butcher was investigated. The three flagellates show minor changes (15–60%) in enzyme activities when ammonium is replaced by nitrate as the nitrogen source or the concentration of nitrogen is lowered from 2 to 0·2 mM. The activities of NADH-GDH and NADPH-GDH in the three flagellates do not appear to be high enough to make a significant contribution to ammonium assimilation in the presence of a highly active GS. Fast protein liquid chromatography (FPLC) of GS revealed the presence of two distinct molecular forms, designated as GS1 and GS2, in C. pulsatilla and T. suecica, whereas only a single GS peak designated as GS2 was detected in B. submarina. Both GS1 and GS2 are stabilized by sorbitol and glycinebetaine in media employed for enzyme extraction and FPLC fractionation. The presence of thiol reagents is essential for GS2 stability, but inhibits GS1 activity. GS2 is by far the more active of the two isoenzymes in C. pulsatilla and T. suecica. This isoenzyme, therefore, appears to be the major port of entry of ammonium in all three flagellates.