The ichthyotoxic Cochlodinium polykrikoides is one of the most harmful bloom-forming dinoflagellates. In the present study, the economically important red seabream Pagrus major was exposed to sublethal concentrations of C. polykrikoides (i.e., 1,000 and 3,000 cells mL−1) for 24 h, and the antioxidant defense system and DNA damage dose-specific responses were analyzed during the exposure and additional depuration period (2 h) in the gill tissue. No significant ichthyotoxicity was observed under different light and dark conditions, while significantly lower levels of opercular respiratory rate were measured in the C. polykrikoides-exposed red seabream. Intracellular malondialdehyde (MDA) content increased significantly in the 3,000 cells-exposed gill tissues at 24 h and the increased level was maintained during depuration. Intracellular glutathione (GSH) levels were significantly depleted following exposure to 3,000 cells mL-1 of C. polykrikoides, but the levels increased significantly in the depuration phase. Overall, significantly higher activity of antioxidant defense system enzymes such as catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GR), and glutathione peroxidase (GPx) were observed in the 3,000 cells mL−1-exposed gill tissues at 24 h and during depuration. Analysis of the two reliable DNA damage parameters, Olive tail moment and percent tail DNA, showed significantly elevated levels of DNA damage in the 1,000 and 3,000 cells mL−1-exposed gill tissue. Increases in the activity of the antioxidant defense system and DNA damage may be one of the major mechanisms mediating C. polykrikoides-induced devastation in aquaculture and fisheries.