This study investigated the effects of paraquat, a widely used herbicide, on the aquatic unicellular alga Chlorella vulgaris through short-term toxicity tests at the physiological and gene transcriptional levels. Exposure to 0.5 microM paraquat increased the activities of the antioxidant enzymes superoxide dismutase, peroxidase, and catalase to levels 4.93, 3.19, and 3.09 times higher, respectively, than those of the control. Furthermore, exposure to 0.75 microM paraquat increased the activities of these antioxidant enzymes to even higher levels. The decrease in chlorophyll content and the increases in reactive oxygen species (ROS) and malondialdehyde content following exposure to paraquat suggest that the alga was severely damaged and cell growth was greatly inhibited. Real-time PCR showed that paraquat reduced the transcript abundance of psaB and rbcL to 7.09 and 29.83% of the control, respectively. Our results demonstrate that paraquat inhibited electron transport and CO2 assimilation, and also triggered the synthesis of ROS that disrupt cellular structure and inhibit cell growth.