Background <p>Flatfish metamorphosis involves dramatic tissue remodeling, including the migration of one eye to the opposite side of the body, enabling the transition from pelagic to benthic life. While this process requires precise transcriptional regulation, the role of epigenetic mechanisms remains poorly understood. Here, we investigate DNA methylation dynamics during turbot metamorphosis using reduced-representation bisulfite sequencing (RRBS) across three key stages: pre-metamorphosis, climax, and post-metamorphosis.</p> Results <p>We identified stage-specific methylation patterns, with more than 31% of hypermethylated regions emerging during the climax phase—coinciding with upregulated <i>dnmt3a</i> (<i>de novo</i> methyltransferase) and altered expression of photoreceptor adaptation genes. Critically, the migrating and non-migrating eyes exhibited divergent methylation and expression of retinal ganglion cell (RGC) regulators (<i>eomesa</i>, <i>tbr1b</i>), linking epigenetic changes to asymmetric ocular development.</p> Conclusion <p>Our results suggest that DNA methylation may play a role in visual system remodeling, particularly in processes associated with RGC-mediated eye migration and light-sensing adaptation, providing new understanding of the epigenetic regulation of vertebrate metamorphosis.</p>