The Roatán Spiny-tailed Iguana (Ctenosaura oedirhina) is an endangered species endemic to only two islands in the Bay of Honduras and a few of its surrounding cays. Ctenosaura oedirhina is currently threatened by different impacts, including habitat modification, invasive predators, and illegal collection and harvesting. Although previous work has monitored population numbers, animal distributions, and genetic variation, very little is known about the reproductive ecology and physiology of the species. Physiological indicators provide valuable information regarding the health of animals and populations. Commonly used metrics include circulating hormone concentrations, energetic indicators, and immunological indices. However, the aforementioned physiological measures can also be difficult to interpret because they are not static but rather vary according to sex, season, reproductive state, and body condition. Therefore, to understand the health status of an individual better, it is important to concomitantly measure multiple related and relevant physiological systems, and to examine these responses under different individual and environmental contexts (e.g., reproductive state, site). In the current study, we measured circulating plasma oxidative stress markers and energy metabolites in five populations of Roatán Spiny-tailed Iguanas during the prenesting season. We found significant physiological variation in females according to breeding state, and males according to population. Understanding the natural variation in the physiology of free-living animals will allow us to determine the significance of physiological measures such as health indicators in the future and thus better manage these threatened populations.