As a by-product of cotton production, cottonseed protein is a sustainable source of high quality, plant-based protein that is widely available wherever cotton is grown. Unfortunately, the 11 million metric tons of cottonseed protein produced by the global cotton crop every year is mostly used in ruminant feeds due to presence of the anti-nutrient, gossypol. Cottonseed protein can be fed to non-ruminant species including aquaculture, but care must be taken to stay within the safe limits for gossypol. For several decades the cottonseed industry has been continuously working towards efforts to mitigate the negative effects of gossypol, however a commercially viable technology has been elusive. Chemical, physical and biological techniques are all effective at removing gossypol at laboratory scale, but scaling up to commercial production has not yet been accomplished. Considerable research has shown that cottonseed protein is not only very palatable, but it can also extend the use of the fish meal in aquaculture diets, if the safe levels of inclusion are not exceeded. Every species has a different tolerance for gossypol. For example, research has shown that shrimp can tolerate 1600 ppm gossypol in the diet, whereas performance in trout tends to decline when gossypol exceeds 250 ppm. Gossypol’s biological activity is not only variable among species, but is also dependent on age, stress level and other dietary factors that interact with gossypol affecting its absorption and biological activity. It is possible to add ferrous sulfate (iron) to the diet to help reduce the absorption of gossypol, however, while the use of iron to increase cottonseed protein inclusion in the diet has been well documented in several monogastric species, gossypol limitations and the use of additional iron to the diet needs to be thoroughly investigated, in individual aquaculture species, before specific recommendations can be made to ensure safe use of cottonseed protein products in aquaculture feeds.