Livestock species offer a unique opportunity to trace genetic and epigenetic evolutionary trajectories. Genetic variation through time is well studied whereas in epigenetics it is insufficiently known. Yet epigenetic changes and their potential transmissibility across multiple generations is crucial, especially in the current context of adaptation to contemporary challenges for more animal resilience to climate change, reduced resource use and environmental impact. In this study we aim to better grasp the evolution of epigenetic patterns and their link to genetic variation. We had access to a dataset from two decades of selection, 15 continuous generations, for a sino-european pig breed. For each generation we sampled a pool of sperm from the most influential boars. Recent technological developments from Oxford Nanopore Technology provided us with high quality sequencing for both the genome and the epigenome. For each sample we obtained whole genome sequences with 30X coverage and the methylation status for about 30 million CpG sites, which is the full information on CpG for Sus scrofa genome (GCF 000003025.6). We identified regions showing changes in methylation status across generations and we clustered CpG sites having similar evolution with the objective to see variation along the genome and through time. Additionally we inferred the correlation between genetic and epigenetic changes. These results will contribute to the development of a statistical model to identify epigenetic selection signatures and to adjust selection models to include multi and transgenerational epigenetic changes, thus better accounting for the non genetic heritability in selection decisions.