During winter hibernation, body temperature falls to near ambient levels, metabolism is shifted to favor lipid oxidation and transcriptional and translational activity is minimized in the face of limited resources and increased heat generation costs. In order to regulate such profound changes, mammals require control at least partly brought about by protein post-translational modifications. Protein lysine methylation provides a mechanism by which enzymes may alter the activity, stability and modification states of proteins relevant to hibernator physiology. Protein abundance of SMYD2, SUV39H1, SET8, SET7/9, G9a, ASH2L and RBBP5 in 13-lined ground squirrel (Ictidomys tridecemlineatus) skeletal muscle and liver was characterized. Tissue-specific regulation was seen and enzymes changed during either torpor, arousal, or transitory periods. Methylation of H3, HSP90, and p53 proteins were also quantified and typically followed patterns of modifying enzymes. Overall, these experiments show protein lysine methylation is differentially regulated during 13-lined ground squirrel hibernation.