Abstract: The gill tissue of cobia (Rachycentron canadum) is sensitive to water temperature changes. In order to investigate the effect of low temperature stress on juvenile cobia, and reveal its response mechanism to low temperature stress, we designed two low temperature groups (18 ℃ and 21 ℃) and one control group (28 ℃), to analyze the antioxidant responses, expression of apoptosis-related genes and histological structure of the gills on 0, 4^th and 7^th day after the stress. The results show that the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) in the low-temperature groups were significantly lower than those in the control group (P<0.05), while the malondialdehyde (MDA) mass concentration in the low-temperature groups was significantly higher than that in the control group (P<0.05). The expression of apoptosis-related genes bax, caspase-9, caspase-3, p53 and mdm2 increased significantly in the low-temperature groups, while the expression of Bcl-2 decreased significantly on 4^th and 7^th day (P<0.05). The TUNEL results reveal that low-temperature treatment increased the cell apoptosis rate of the gills, and caused lesions including fusion of secondary lamellae, necrosis of epithelial cell and hyperplasia of chloride cells. The results indicate that low-temperature stress causes oxidative stress, induces apoptosis and damages the structural integrity of the gills, which suggests that normal physiological functions of juvenile cobia can be affected by low temperature significantly.