The toxic effects of different gradient concentrations of Hg2+ and Cd2+ on chlorophyll content, chlorophyll a/b value, photosynthetic O-2 evolution, respiration rate, anti-oxidase system (superoxide dismulase (SOD), catalase (CAT), peroxidase (POD)) and ultrastructure of the cells of Azolla imbricata (Roxb.) Nakai were studied. The results showed that with Hg2+ and Cd2+ increase, chlorophyll content and chlorophyll a/b value, photosynthetic O-2 evolution decreased drastically; respiration rate peaked at 2 mg/L pollutant and declined afterwards. The activities of SOD, CAT and POD increased first and decreased afterwards except the activity of POD, which decreased with the increasing of Cd2+ concentration. Ultrastructural observation showed that the extent of ultrastructural damage was much more serious with higher pollutant concentration and longer time of stress. This resulted in swelling of chloroplast, disruption and disappearance of chloroplast membrane and disintegration of chloroplasts; swelling of cristae of mitochondria, deformation and vacuolization of mitochondria; condensation of chromatin in nucleus, dispersion of nucleolus and disruption of nuclear membrane. The experimental results showed: (1) Hg2+ and Cd2+ pollution not only destroyed physiological activities, but also caused irreversible damage to its ultrastructure, thus leading the cells to death; (2) With increase in the stress of Hg2+ and Cd2+, ultrastructural damage was related to the changes of plant physiology; (3) The toxic symptoms of plant showed an evident correlation between dose and effect; (4) The toxicity of Cd2+ on A. imbricata is heavier than that of Hg2+ under the same treatment time and concentration. The lethal concentration of Hg2+ to A. imbricata ranged from 3.5 to 4 mg/L, and that of Cd2+ ranged from 3 to 3.5 mg/L. The damage of cell ultrastructure on Anabaena azollae Strasburger was observed. The results indicated that tolerance of Azolla imbricata for Hg2+ and Cd2+ was higher than that of A. imbricata.