Aquaculture is currently the fastest growing food-producing sector in the world. The growth of this industry has been rapid for the last 25 years, however, aquaculture still relies heavily on feed input from wild capture fisheries. Landings in wild capture fisheries have been stagnant for the last two decades; therefore, new alternatives for conventional fish meal and fish oil need to be found. In this review, various alternatives are described and their advantages and disadvantages are evaluated. Single cell oils (SCO) and single cell proteins (SCP) produced by microorganisms are recognized as the alternative with the most potential for replacing fish meal and fish oil in aquacultures. However, production costs of SCOs and SCPs are still higher than production costs of Omega-3 rich oils from other sources (wild capture, plant derived oils and genetically modified plants); therefore, currently used substrates need to be replaced with cheaper agriculture and industrial biomass residues applicable for microbial fermentation. In order to evaluate various biodegradable residues and find the most suitable ones for SCO and SCP production, methods analysing resource availability are reviewed.