Dissolved oxygen (DO) in the culture water is an important environmental factor in fish farming. This study tested whether genetically improved farmed tilapia (GIFT, Oreochromis niloticus) challenged with a hypoxic episode would show inhibited growth, increased metabolic stress and a reduced immune response. GIFT subjected to 72 hr of semi-lethal hypoxia (determined by linear regression as DO = 0.64 mg/L) showed changes in blood biochemistry, energy metabolism and related immune responses. In the early stages of stress, GIFT showed increased anaerobic respiration and increased lactic acid accumulation. Compared with a control group, white and red blood cell counts, hematocrit and blood hemoglobin concentration in GIFT exposed to 4 hr of semi-lethal hypoxic stress were not significantly changed. However, the levels of glutamic-pyruvic transaminase, glucose, cholesterol and cortisol were significantly higher under hypoxic stress at 2 and 4 hr. In the later stages of stress, GIFT displayed increased oxygen utilization and increased aerobic respiration associated with increased red blood cell count, hematocrit and hemoglobin concentration. However, the white blood cell count, serum lysozyme and complement C3 activities began to decline, associated with increased mortality. Reverting to a normal DO environment (5.0 mg/L) for an additional 72 hr, GIFT showed strong recovery, with respiratory metabolic enzymes, immune indicators and associated energy metabolites restored to near normal levels. Our observations contribute to a better understanding of the mechanisms of energy and immune regulation in fish, and will help reduce the damage caused by hypoxic stress during culture.