The decline in dissolved oxygen concentrations has been one of the most important changes occurring in the oceans, greatly impacting the survival, abundance, development, metabolism, growth, and reproduction of aquatic organisms. Aquaculture has suffered from coastal seawater deoxygenation, and the micro-environments of aquaculture systems also contribute to the frequent occurrence of hypoxic events. The cultivation of hypoxic-tolerant species and varieties will be urgent for the sustainable development of aquaculture. In this review, the current and ongoing research topics on hypoxia tolerance of aquatic animals were summarized and discussed, including the physiological mechanisms of hypoxia tolerance and the genetic and epigenetic sources of hypoxia tolerance differences in aquatic animals. Understanding the results of these two aspects will allow us to shape aquatic animals' tolerance to hypoxia and create hypoxia-tolerant aquaculture species and varieties by cutting-edge breeding techniques. This will help us alleviate the ecological damage and economic losses brought on by hypoxia occurrences. We urge those working in the aquaculture field to understand the negative effect that hypoxia has on aquaculture systems. We also encourage future research that uses aquaculture systems as ones of the models for studying environmental hypoxia and biological hypoxia responses and adaptation. [ABSTRACT FROM AUTHOR]