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Aquaculture is the fastest growing animal producing sector in the world and is expected to play an important role in global food supply. Along with this growth, concerns have been raised about the environmental effects of escapees and pollution, fish welfare, and consumer health as well as the use of marine resources for producing fish feed. In this paper we present some of the major challenges salmon farming is facing today. We discuss issues of relevance to how to ensure sustainability, by focusing on animal production systems, breeding approaches, sources for feed ingredients, and genetic engineering strategies. Other crucial issues such as animal welfare, environmental quality, and ethics are elaborated with regard to relevance for the sustainability of aquaculture. Additionally, we comment on socio-economic distributive implications by intellectual property rights (IPR) strategies on access to genetic material and traceability. To improve sustainability of salmon farming we suggest that there is a need for new approaches to guide research, for identification of ethical issues, and for engaging stakeholders in resolving these challenges.