Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not yet been clarified. We have investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. The response to a three-month supervised one-legged knee-extension endurance training program (n=23) was evaluated using performance tests and metabolic enzyme activity assays. DNA methylation and transcriptomic profiling were performed on vastus lateralis muscle biopsies, using Illumina 450k beadchip and RNA-seq. Transcriptome data was investigated for a subset of the subjects (n=12) that participated in a follow-up training intervention one year later training both legs, one at a time, at exactly the same work load as the first period. A signature of DNA methylation and gene expression separated the samples based on training and gender. The training effects were mirrored by alterations in DNA methylation and gene expression. We detected 4919 differentially methylated positions (DMPs) and 4076 differentially expressed genes (FDR<0.05). DMPs were predominantly found in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. Ontology analysis demonstrated that muscle related processes e.g. myogenesis, muscle energetics and tissue remodelling were enriched. The analysis identified transcriptional regulator binding motifs of Myogenic Regulatory Factors, Myocyte Enhancer Factor 2 and the ETS group in the proximity of DMPs. An integrative analysis identified positive or negative correlations between methylation and expression, suggesting coordinated training-induced modifications. A transcriptional network analysis revealed modules with distinct ontologies, and the overall direction of methylation changes within each module was inversely correlated to expression changes, lending further support to a coordination between the epigenome and the transcriptome. From second training period, we found neither evidence of any remaining transcriptome effects from the first training period, nor any difference in response between the previously trained leg compared to the previously untrained leg. In conclusion, this data provides a valuable and novel perspective on the fields of human physiology and environmental epigenomics, showing that a physiological stimulus can induce highly consistent and associated modifications in methylation and expression concordant with the observed health-enhancing phenotypic adaptations. This could represent a mechanism for variability in individual response to lifestyle interventions or disease susceptibility.