Vancouver Island marmots (Marmota vancouverensis) (VIMs) are critically endangered fat-storing hibernators. Besides in-situ conservation efforts, a captive breeding and release program started in 1997. Compared to wild individuals, captive VIMs have increased adiposity, reduced hibernation length, and suffer from cardiovascular disease. Hibernation duration, body weight, and reproductive success of captive VIMs from 1997 to 2018 were reviewed. The number of winters spent in captivity, the origin of the marmot (captive‐ or wild‐born), the facility, and the weight all had a significant effect on hibernation length. Captive, wild‐born marmots hibernated for longer than captive‐born by 21 ± 2 days. The odds of successful breeding were increased by 20% for every 10 additional days of hibernation. To investigate differences in lipid metabolism between wild and captive VIMs, serum α-tocopherol and leptin, and plasma and white adipose tissue (WAT) fatty acid (FA) profiles were compared. The total FA concentration, n-6/n-3 ratio, saturated FAs, and n-6 polyunsaturated FAs (PUFAs) were significantly higher in captive marmots, whereas n-3 PUFAs and the HUFA score were higher in wild marmots. Serum concentrations of α-tocopherol were greater by an average of 45% in captive marmots, whereas leptin concentrations did not vary. Woodchucks were used as a model to assess the effects of varying the dietary n-6/n-3 PUFA ratio throughout the active season, mimicking the expected changes occurring in wild VIM diet. Body composition, weight, hibernation robustness, circulating leptin, adiponectin, and α-tocopherol levels, and WAT and plasma FA profiles were compared between two groups. One group (TZ) was fed pellets with a n-6/n-3 ratio of 4.3 throughout the active season and the other (MRP) was fed pellets with a n-6/n-3 ratio of 1.7 for the first half of the active season and then a ratio of 4.3 for the subsequent half. Although the diet was not found to influence body composition, weight, or hibernation robustness, the MRP diet provided woodchucks with a FA profile resembling that of wild marmot species. Leptin concentration significantly changed between times points and groups with the MRP group showing lower leptin concentrations compared to the TZ group by an average of 384 pg/mL in early August.