Abstract Background: While the stress response inspired genome-wide epigenetic studies in vertebrate models, it remains mostly ignored in fish. We modified the epiGBS (epiGenotyping By sequencing) technique to explore changes in genome-wide cytosine methylation to a repeated acute stress challenge in the nucleated red blood cells (RBCs) of the European sea bass (Dicentrarchus labrax). This species is widely studied in both the natural and farmed environments, including issues regarding health and welfare.Results: We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appear to manifest after the stress challenge. Only, fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct stress-related genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-stress individuals. However, literature surveys indicated that 38 of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear especially relevant to integrate a centrally produced stress response.Conclusion: By putting forward DMCs associated to stress-related genes, we show that minimally invasive RBCs deserve more attention to investigate the epigenetic response to stress and components of the stress response without sacrificing fish. In parallel to blood parameter measurements (e.g. cortisol, glucose levels), and other molecular approaches (e.g. gene expression variation), features of the epigenetic landscape may offer new opportunities for biomonitoring components of the stress response in fish.