Domestication and selective breeding of the major commercial fish species are essential to enable sustainability of the rapidly expanding aquaculture sector. The existing improvement programmes are based exclusively on genetic markers, overlooking the fact that selection for complex traits is strongly affected by environmental conditions and that epigenetics likely account for a large proportion of the observed phenotypic variation. Non-coding RNAs (e.g., miRNAs) and cytosine methylation (5mC) and hydroxymethylation (5hmC) of DNA are key mechanisms underlying epigenetic regulation of gene expression. We have recently identified a panel of 5mCs, 5hmCs and miRNAs that are potential epigenetic markers (epimarkers) of improved growth in Nile tilapia (Oreochromis niloticus). EPIMARK will evaluate the commercial feasibility of our novel kit of growth epimarkers, so that they can be applied in selective breeding programmes. This will be achieved by (i) validating the miRNA, 5mC and 5hmC epimarkers, (ii) developing an assay for their quantification, (iii) investigating the commercial and financial feasibility and (iv) developing the optimal business strategy, consolidated in a business plan. The EPIMARK kit will lead to a more efficient selection of fish in breeding programs based on growth potential, thereby increasing the profitability and sustainability of the aquaculture industry. The technology developed in EPIMARK will also open important avenues of innovation, including the use of epimarkers for selection of other superior production traits and disease resistance in Nile tilapia and in other species of commercial importance.