Hypoxia is currently one of the greatest threats to coastal ecosystems worldwide, generating massive mortality of marine organisms, loss of benthic ecosystems and a decrease in fishery production. We evaluated and compared the tolerance to hypoxia of two species from different habitats of the Peruvian coast, the Peruvian rock seabass Paralabrax humeralis and the Peruvian grunt Anisotremus scapularis. The effect of hypoxia was measured as a function of the exposure time (progressive and chronic) on the behavioural and physiological responses of the two species, as well as on the enzymatic activity associated with the oxidative stress response of lactate dehydrogenase (LDH), superoxide dismutase (SOD) and alkaline phosphatase (AKP). The ventilatory frequency was measured at two different temperatures (16 and 22°C) under progressive hypoxia conditions to determine the ventilatory critical point (Vcp). A. scapularis showed a higher Vcp than P. humeralis, which was positively affected by temperature. The median lethal time of A. scapularis was 36 min at 60% of oxygen saturation, while P. humeralis showed no mortality after 31 days of exposure at 5% oxygen saturation. Different enzymatic activity (P < 0.05) between species under hypoxia was recorded, in SOD (gill and muscle) and AKP (blood). A general tendency, under hypoxia, to slightly increase LDH activity (except for blood in A. scapularis, P < 0.05) and SOD activity (mainly in muscle of A. scapularis, P < 0.05), and decrease AKP activity (mainly in liver of P. humeralis, P < 0.05) was observed. The response of P. humeralis to hypoxia goes through a reduction in activity and metabolism, so this species can be considered hypoxia-tolerant, allowing it to face hypoxia events during prolonged periods. On the other hand, A. scapularis response to hypoxia prioritizes avoidance mechanisms and, together with other adaptations, makes it especially vulnerable to hypoxia and able to be considered hypoxia-intolerant.