This study evaluated the effect of different doses of the antioxidant α-lipoic acid (LA) administered by intraperitoneal injection on the detoxifying capacity (activity of glutathione-S-transferase, GST) and oxidative damage (lipids and proteins) in the pompano, Trachinotus marginatus. The plasma glucose levels showed that there were no differences between the treatments (P > 0.05). In the brain, GST activity was significantly higher (P < 0.05) in fish injected with 40 mg LA kg−1 when compared with the control group. In the muscle, GST activity was not influenced by LA treatment (P > 0.05). In the liver, fish injected with 20 mg LA kg−1 showed higher GST activity than the control group (P < 0.05); however, higher doses (40 and 60 mg LA kg−1) led to a reduction of GST activity in the liver, which was comparable to that observed in the control group (P > 0.05). The two highest LA doses (40 and 60 mg kg−1) had opposite effects, depending on the tissue examined: LA was an antioxidant in the brain, reducing lipid peroxidation (P < 0.05), and a pro-oxidant in the liver, augmenting oxidative lipid damage (P < 0.05). The latter effect was accompanied by an increase in the free iron concentration in the liver at higher LA doses. These results indicate the need to thoroughly evaluate the antioxidant effects on aquatic organisms, since at some doses and/or in some organs their beneficial effects can be lost.