Atlantic salmon ( Salmo salar ) populations have been declining across the North Atlantic, with southern populations, including those in rivers draining into the southwestern Bay of Biscay, showing some of the strongest impacts. These rivers mark the species' southernmost distribution limit and are highly vulnerable to global change stressors such as rising marine and freshwater temperatures, ocean acidification, altered food webs, and pollution. Epigenetic mechanisms, including DNA methylation, can mediate environmentally induced phenotypic plasticity and may contribute to rapid adaptation. We used Reduced Representation Bisulphite Sequencing (RRBS) to examine genome‐wide, single‐base DNA methylation patterns in fin tissue from Atlantic salmon sampled at three time points over two decades (early 2000s, early 2010s and early 2020s) from two river systems (Nalón–Narcea and Sella, northern Spain). Analysis of 715,240 common CpGs in 120 adults identified differentially methylated cytosines (DMCs) and regions (DMRs), including the promoters of two Hox genes essential for embryonic development. Gene Ontology and KEGG enrichment analyses revealed significant overrepresentation of developmental pathways, notably the ECM–receptor interaction pathway involved in morphogenesis and vertebral formation. Several enriched pathways were also related to environmental information processing and cell signalling, suggesting a potential epigenetic response to environmental stressors. These findings provide evidence of an epigenetic footprint of environmental change over time. DNA methylation may influence phenotypic variation in declining southern salmon populations, which might facilitate adaptation. Future research should incorporate controlled experiments to link methylation changes to specific stressors and assess their causal role in resilience and adaptation.