We determined the intracellular contents and concentrations of cysteine and glutathione in five species of marine phytoplankton, Tetraselmis tetrathele (West) Butcher (Prasinophyceae), Porphyridium purpureum (Bory) Drew et Ross (Rhodophyceae), Pavlova sp. (Haptophyceae), Isochrysis sp. (Haptophyceae), and Pleurochrysis carterae (Braarud et Fagerl) Christensen (Haptophyceae), and examined relationships to mercury susceptibility. Intracellular contents (concentrations) of nonprotein thiols in the five species ranged from 119 to 1210 amol (0.66–12.0 mM) for cysteine, 78 to 719 amol (0.65–2.52 mM) for cystine, 31 to 677 amol (0.13–1.25 mM) for reduced glutathione (GSH), and 12 to 123 amol (0.15–0.26 mM) for oxidized glutathione (GSSG). The intracellular contents of the nonprotein thiols were not proportional to the intracellular concentrations because the cell sizes differed. Oxidation ratios of cysteine:cystine and GSH:GSSG were also wide ranging in the five species, and the higher the concentration of the reduced form of nonprotein thiols, the less they tended to be oxidized. Flow cytometric analyses with fluorescein diacetate were used to monitor the effect of HgCl2 on esterase, and the 50% effect concentrations (EC50) were compared in the five species. The EC50 after 3 h exposure to HgCl2 correlated well with the GSH concentrations but not with those of cysteine. These results indicate that the intracellular concentrations of the nonprotein thiols reflect antioxidant activity and susceptibility to heavy metals.