Short-term (24h) experiments were performed to examine the effect of anthraquinone (ANTQ) and phenanthrenequinone (PHEQ) on two Scenedesmus armatus strains (B1-76 and 276-4d) grown in a batch culture system aerated with CO2 at a low (0.1%) or elevated (2%) concentration. ANTQ at concentrations within the range of 0.156-1.250 mg dm-3 inhibited the growth of B1-76 population in a concentration-dependent manner, and calculated EC50 for low-CO2 cells was 0.56 mg dm-3. The toxic effect of ANTQ on this strain was more pronounced in high-CO2 cells, where not only growth but also photosynthesis, respiration and SOD activity were significantly inhibited. In contrast, except for SOD activity, no ANTQ effects on strain 276-4d were found. PHEQ at concentrations within the range of 0.063-0.125 mg dm-3 inhibited the growth of B1-76 population in a concentration-dependent manner. The value of EC50 for low-CO2 B1-76 cells was 0.10 mg dm-3. PHEQ inhibited the growth of both strains regardless of CO2 concentration. In B1-76 cells affected by PHEQ, inhibition of photosynthesis was independent of the CO2 level, whereas the SOD activity was much higher in cultures aerated with 2% than with 0.1% CO2. Higher toxicity of PHEQ to strain 276-4d grown at 2% CO2 was accompanied by strong inhibition of photosynthesis, while in low-CO2 cells this process was slightly stimulated. The SOD activity in both low- and high-CO2 cells of strain 276-4d treated with PHEQ was 2-3 times higher compared with the controls. The pattern of SOD isoforms (PAGE analysis) obtained from cells exposed to ANTQ or PHEQ did not change compared with the controls, but the location of the SOD isoforms bands on gel was affected by the concentration of CO2. The results suggest that the strain-specific toxicity of ANTQ and PHEQ may result from oxidative stress. In addition, carbon dioxide appears to play an important role in the toxicity of quinones to algae.