Aquaculture production is currently challenged to meet the growing demands for seafood protein throughout the world. To achieve this growth in an efficient, safe and sustainable manner, novel tools and applications will need to be incorporated at each step of the production line. A variety of ‘omics’ (e.g. transcriptomics, proteomics, metabolomics) applications have already begun to emerge in aquaculture research with extreme success. A promising new ‘omics’ approach is metabolomics, which aims to use metabolite profiles to identify biomarkers indicative of physiological responses of living samples (e.g. whole organism, tissues, cells) to environmental or culture conditions. One of the benefits of this approach is that it uses a broad scan of biological conditions to identify often unexpected problem or risk areas upon which to focus management attention. In this contribution, we have selected relevant research examples to showcase the applications of metabolomics in aquaculture in four major areas: hatchery production, nutrition and diet, disease and immunology, and post-harvest quality control. The novelty of this approach is highlighted by the fact that we cite the majority of published papers in this field, and they are all recent (within the last decade) contributions.