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Dissolved oxygen (DO) and temperature are the potential immunomodulators in fish and play the important roles in regulating immunity. We studied the effect of intermittent hypoxia under different temperature on the immunomodulation in vaccinated Nile tilapia (Oreochromis niloticus). The expression of immune-related genes, enzymatic activities, histology, cumulative mortality, and S. agalactiae clearance were assessed. Study conditions were intermittently hypoxic (4.0±1.0mg/L DO) at 30±0.5°C or 35±0.5°C. Interleukin-1beta (IL-1β), tumor necrosis factor alpha (TNF-α) and gamma interferon (IFN-γ) mRNA expression in spleen and head kidney were significantly lower in vaccinated hypoxic fish compared to the vaccinated normoxic fish. Levels of heat shock protein 70 (HSP70) in tissues showed an opposite tendency. Superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) activities were significantly lower in vaccinated hypoxic fish. Malondialdehyde levels were significantly greater under hypoxic conditions. In vitro studies evaluated the effects of intermittent hypoxia at different temperatures on cells of vaccinated O. niloticus. Phagocytic activity of peripheral blood leucocytes (PBLs) and intracellular reactive oxygen species (ROS) production in head kidney cells were significantly decreased by intermittent hypoxia at either 30°C or 35°C, while nitric oxide levels in tissues cells increased significantly under hypoxic conditions. These changes were well reflected by the further suppression modulation on S. agalactiae clearance in vaccinated O. niloticus and higher cumulative mortality by intermittent hypoxia. Taken together, intermittent hypoxia at either 30°C or 35°C could suppress immunomodulation in vaccinated Nile tilapia.Intermittent hypoxia at either 30°C or 35°C modulates immune genes expression.Enzymatic activities were lower in vaccinated hypoxia fish at both temperatures.Phagocytosis and ROS production decreased in vaccinated hypoxia fish.Cumulative mortality was higher in vaccinated hypoxia fish.Spleen, head kidney and brain bacteria burden was lower in vaccinated normoxic fish.