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When captured, free‐living crocodilians respond by hyperstimulation of the hypothalamic‐pituitary‐adrenal (HPA) axis, which triggers a cascade of downstream events of physiological stress. We examined these responses in two unstressed, and stressed Amazonian caimans, Caiman crocodilus and Melanosuchus niger. Plasma corticosterone levels increased in both stressed caiman species. In M. niger, the levels of this hormone increased 5.2‐fold compared with the basal range values, while in C. crocodilus this was only 1.7‐fold. After stress, M. niger needed more than 6 h to return its corticosterone levels to basal range values, whereas in C. crocodilus just 0.5 h was enough. Downstream events were characterized by an increase in glucose levels, which is associated with corticosterone increments. Excessive muscle activity resulted in increased plasma lactate content in both species. Lactate levels were also related to plasma calcium concentration, possibly due to the buffering capacity for preventing lactic acidosis. Clearance of excessive lactate load was faster in M. niger (0.5 h) than in C. crocodilus (more than 6 h). Although both caiman species respond in the same way to capture, the amplitude and duration of activation of the HPA axis are different. M. niger may be potentially more sensitive to acute stress than C. crocodilus. On the other hand, C. crocodilus needs more time to recover from the lactic acid load. Our experiment provides a useful diagnostic tool for management and conservation programs, as well as evaluating the impacts of tourism and recreational capture on caimans in the Amazon. Highlights: In both stressed species, capture stress resulted in increased plasma corticosterone, glucose, lactate, and calcium levels.The physiological responses observed in Melanosuchus niger indicate that it is more susceptible to acute stress conditions. [ABSTRACT FROM AUTHOR]