Epigenetic regulation through the methylation of genomic cytosine nucleotides is a crucial component in the regulation of gene expression. DNA methylation in mammalian genomes serves as an important modulator of when and where a gene should be expressed, by primarily targeting 5'-CpG-3' dinucleotides which have been associated with gene regulatory sites, including promoter sequences. Food deprivation in mammals is associated with increases in reverse triiodothyronine (rT3), an inactive form of the metabolism driving thyroid hormone triiodothyronine (T3), as a direct consequence of increases in the expression of the gene deiodinase type 3 (DI3). However, in prolong-fasted, metabolically active elephant seal pups, cellular thyroid hormone-mediated components are up-regulated with fasting duration, while rT3 levels remain low. To address our hypothesis that methylation status of DI3 contributes to the silencing of a gene that would otherwise be expressed under such physiological conditions, we infused early fasted pups with thyroid stimulating hormone (TSH), extracted and treated genomic DNA with sodium bisulfite in an effort to detect and quantify 5-methylcytosine (5mCs) at single base-pair resolution. In reference to the genomic sequence of DI3 in elephant seals, prior to infusion with TSH, there is 50% methylation of 15/30 CpG sites in adipose tissue. Twenty-four hours post infusion with TSH, the degree of methylation of DI3 increases to 93%, with methylation observed in 27/29 CpG sites. Moreover, in muscle, methylation reaches 90%, with 26/29 CpG sites being methylated at only 60 minutes post-infusion with TSH, suggesting a tissue specific sensitivity. Aside from providing an initial and novel assessment of methylation regulation and status in elephant seals, the data demonstrates a unique adaptation to a methylation pattern where the compacted chromatin structure of DI3 plays a crucial role in suppressing the normal physiological response to fasting otherwise present in most mammals.