The four experimental groups were set up to test the response of Carassius auratus and Ctenopharyngodon idella to ammonia toxicity and taurine within 96 h. Group 1 was injected with NaCl, group 2 was injected with ammonium acetate (C. auratus 7 mmol/g; C. idella 9 mmol/g), group 3 was injected with ammonium acetate and taurine (100 μg/g), and group 4 was injected with taurine. C. auratus in group 2 had lower mRNA expression of SOD, CuZnSOD and CAT in liver than those of tested fish in groups 1 and 3; tested fish in groups 2 and 3 had lower mRNA expression of GPx in liver than that in group 1; the highest mRNA expression of SOD, CuZnSOD, CAT and GPx in brain were found in group 1; C. idella in groups 2 had higher mRNA expression of SOD, CuZnSOD, CAT and GPx in liver; fish in groups 2 and 4 had lower mRNA expression of SOD and CuZnSOD in brain than those in groups 1 and 3; fish in group 3 had the highest mRNA expression of CAT and GPx in brain. C. auratus and C. idella in group 2 had the highest mRNA expression of TNF and IL in the brain and liver. This study indicates that defensive strategies are more effectively on C. idella in dealing with the ammonia challenge compared with C. auratus; the taurine could more effectively mitigate the adverse effect of oxidative stress on C. auratus and C. idella, but the inflammatory response in hyperammonemia C. auratus and C. idella was not alleviated by taurine.