The toxicity of Rac-metolachlor and S-metolachlor on rice (IIYou92, Oryza sativa L.) seedlings was determined and compared in a hydroponics experiment. The elongation of shoot, main root, and the number of lateral roots were inhibited in both Rac- and S-metolachlor treatments. The 96 h- IC50 of Rac- and S-metolachlor were 12.32 and 9.44 μM for shoot, and 4.69 and 1.75 μM for root, respectively. The content of chlorophyll a, chlorophyll b and total chlorophyll of leaf treated by Rac-metolachlor was higher than that treated by S-metolachlor. The activities of superoxide dismutase, peroxidase, cytochrome P450 2E1, glutathione S-transferase, and the content of glutathione increased after herbicide exposure, and the activities or the content was higher in the S-metolachlor treatment than in the exposure to Rac-metolachlor. Ultrastructural studies revealed that Rac- and S-metolachlor had adverse effects on leaf cells, and S-metolachlor treatment caused higher damage.