Hibernation allows individuals to conserve energy during seasonal low temperatures. As the physiological regulation of hibernation is inadequately understood, I examine hibernation using DNA methylation (DNAm). DNAm is the addition of a methyl group to cytosine at cytosine guanine dinucleotide (CpG) sites in the genome. DNAm in promoters can repress gene expression and be influenced by histone modifications. Using the big brown bat, Eptesicus fuscus, I examined how hibernation influences DNAm, independent of age, through comparing DNAm from bats that differed in hibernation history and comparing DNAm from the same individual between hibernating and active seasons. Both comparisons found evidence of differential enrichment of genes near significant CpG sites resulting from hibernation. The latter analysis found evidence consistent with a histone mark, associated with active transcription, is likely enriched in hibernating bats. These results suggest that DNAm and histone modifications associated with transcription factor binding regulate gene expression during hibernation.