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Juvenile hybrid grouper, Epinephelus lanceolatus ♂ × Epinephelus fuscoguttatus ♀ (mean weight: 26.5 ± 2.8 g, mean length: 11.8 ± 1.3 cm) were exposed to different, sub-lethal levels of waterborne ammonia (0, 1, 2, 4, and 8 mg NH4+/L) for 2 weeks. We assessed the hematological parameters, antioxidant enzymes, and stress responses of juvenile hybrid grouper after 1 week and after 2 weeks. Hematological parameters such as hemoglobin and hematocrit levels, were significantly decreased by ammonia exposure. Plasma components such as the magnesium and total protein contents, and the glutamic oxaloacetic transaminase and glutamic pyruvic transaminase activities were significantly altered by ammonia exposure; however, no changes in the magnesium levels were detected. Antioxidant responses, such as superoxide dismutase and glutathione S-transferase activities, were also significantly affected by ammonia exposure. Stress indicator levels, i.e., plasma cholesterol and heat shock protein 70 levels, were significantly increased by ammonia exposure. The results of this study indicated that ammonia exposure has toxic effects on juvenile hybrid grouper and affects their hematological parameters, antioxidant enzymes, and stress responses.