There is limited ability to biosynthesize long-chain omega-3 fatty acids such as EPA and DHA in food webs leading to humans. Seafood is the key source of ω3 LC-PUFA, with aquaculture expected to meet rising global demand; however, marine fish have a high dietary requirement for EPA and DHA themselves. This was traditionally met using unsustainable dietary fish oil and fish meal, but limited supply and environmental concerns have dictated research on replacements. Among the industrial sources of EPA and DHA, microalgae and especially thraustochytrids stand out as resources with high concentrations. Although unicellular, thraustochytrids are not microalgae as they are not photosynthetic but instead are microheterotrophs. This removes the light requirement and facilitates high yields of monoculture for the production of single-cell oils. The availability, in high concentrations, of usually one or the other essential fatty acid permits a calibration of the EPA and DHA dose, which is especially useful as their effects have mainly been considered together in medical and aquaculture research. EPA and DHA have different effects on cell function and are precursors of different bioactive compounds. Using thraustochytrids, microalgae, and heterotrophic dinoflagellates, the importance of DHA has been investigated. DHA was essential for optimizing the growth of the early life stages of scallops and finfish and was preferentially incorporated into fish membrane phospholipids. The production of microalgae and microheterotrophs can contribute to the treatment of wastewater and waste gas, further enhancing their sustainability and reducing the environmental costs of aquaculture.