In intertidal environments, the recurring hypoxic condition at low tide is one of the main factors affecting fish behaviour, causing broad effects on ecological interactions. We assessed the effects of hypoxia on lateralization (e.g. the tendency to turn left or right), a behaviour related to brain functional asymmetry, which is thought to play a key role in several life history aspects of fish. Using staghorn sculpin (Leptocottus armatus), a benthic fish that typically inhabits the intertidal zone, we found that hypoxia affects behavioural lateralization at the population level. On average, staghorn sculpins showed a distinct preference for right turns under normoxic conditions (>90% oxygen saturation), but an equal probability of turning right or left after exposure to hypoxia for 2 h (20% oxygen saturation). The specific turning preference observed in the staghorn sculpin control population is likely to have an adaptive value, for example in predator-prey interactions by enhancing attack success or survival from predatory attacks. Therefore the alteration of lateralization expressed by staghorn sculpins under hypoxic conditions may have far-reaching implications for species ecology and trophic interactions. Moreover, our work raises the need to study this effect in other species, in which a hypoxia-driven disruption of lateralization could affect a wider range of behaviours, such as social interactions and schooling.