As a result of long-term climate change, regions of the ocean with low oxygen concentrations are predicted to occur more frequently and persist for longer periods of time in the future. When low levels of oxygen are present, this places additional pressure on marine organisms to meet their metabolic requirements, with implications for growth, feeding and reproduction. Extensive research has been carried out on the effects of acute hypoxia, but far less on long-term chronic effects of low oxygen zones, especially with regard to commercially important fishes and shellfishes. To provide further understanding on how commercial species could be affected, the results of relevant experiments must support population and ecosystem models. This is not easy because individual effects are wide-ranging; for example, studies to date have shown that low oxygen zones can affect predator-prey relationships as some species are able to tolerate low oxygen more than others. Some fishes may move away from areas until oxygen levels return to acceptable levels, while others take advantage of a reduced start response in prey fishes and remain in the area to feed. Sessile or less mobile species such as shellfishes are unable to move out of depleted oxygen zones. Some species can tolerate low oxygen levels for only short periods of time, while others are able to acclimatize. To advance the knowledge-base further, a number of promising technological and modelling-based developments and the role of physiological data within these, are proposed. These include advances in remote telemetry (tagging) and sensor technologies, trait-based analyses to provide insight into how whole assemblages might respond in the future, research into long-term adaptability of species, population and ecosystem modelling techniques and quantification of economic effects. In addition, more detailed oxygen monitoring and projections are required to better understand the likely temporal and local-scale changes in oxygen.