Our objective was to elucidate age-related changes in lipids associated with skeletal muscle of Weddell seals and to suggest possible physiological implications. Muscle biopsies were collected from pups, juveniles and adults in McMurdo Sound, Antarctica and analyzed for intramuscular lipid (IML) and triacylglyceride (IMTG) amounts, fatty acid groups, as well as individual fatty acid profiles. The results from this study suggest a switch from primarily saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) in the skeletal muscle of young pups to increases in polyunsaturated fatty acids (PUFAs) as the percentage of blubber increases, resulting in possible thermoregulatory benefits. As Weddell pups continue to develop into juveniles, fatty acids associated with the skeletal muscle changes such that MUFA levels are relatively higher, which may be in response to energy depletion associated with their restricted diving ability and rapid growth. As juveniles transform into adults, a reduction in n-3 PUFA levels in the muscle as the percentage of blubber increases may be indicative of a trigger to prepare for deep diving or could be a mechanism for oxygen conservation during long-duration dives. We speculate that the observed change in lipids associated with the skeletal muscle of Weddell seals is related to ontogenetic differences in thermoregulation and locomotion.