Cadmium (Cd) is a nonessential and toxic trace element widely existed in waters through various anthropogenic activities such as mining and waste disposal. The physiological responses of aquatic organisms to long-term Cd exposure at environmentally relevant concentrations are still not well explored. In the present study, two strains of unicellular green algae Chlamydomonas reinhardtii, a walled strain CC125 and a wall-less strain CC406 were selected to investigate the physiological changes of aquatic organisms after long-term Cd exposure at environmentally relevant concentrations (4.92 and 49.2 g L-1). After about 1,000 generations selection, all of the two strains showed higher intracellular lipid peroxidation and lower photosynthetic activities, and failed to evolve specific adaptation to high level of Cd (4.92 mg L-1) compared to the control. However, short-term low doses Cd exposure exerted hormetic effects on C. reinhardtii and the hormetic stimulation of growth rate, chlorophyll contents and photochemical activities in the lower concentration of Cd (4.92 g L-1) groups were more pronounced than higher ones (49.2 g L-1). Taken together, this study confirmed that long-term exposure to Cd at environmentally relevant concentrations which were regarded as nontoxic in acute experiment would produce toxic effects on C. reinhardtii and should be paid more attention.