Chronic, ongoing stress can impact negatively on health and wellbeing. Indigenous Australians are at an increased risk of experiencing multiple stressors. Hair glucocorticoids have been used as a marker for chronic stress. This study aimed to assess the associations of hair cortisol and cortisone with sociodemographic (age, gender, Indigenous Identification), substance use, emotional wellbeing, and emotional stress, in a cohort at increased risk of stressful events and psychological distress. Cross-sectional data (age 21–28 years) are presented from two Australian longitudinal studies; the Aboriginal Birth Cohort (n = 253) and non-Indigenous Top End Cohort (n = 72). A third of the cohort reported psychological distress, with Indigenous participants reporting higher rates of stressful events compared to non-Indigenous (6 vs. 1; p <.001). Significantly higher levels of cortisone were seen in Indigenous women compared to non-Indigenous women (β 0.21; p =.003). A positive association with age was present in hair cortisol and cortisone in Indigenous young adults (β 0.29 and β 0.41; p <.001, respectively). No association with substance use, emotional wellbeing or emotional stress was seen. Sub-analysis in women suggested a possible curvilinear relationship between hair cortisone and the number of stressful events. In this culturally diverse cohort, hair sampling provides a noninvasive, easily conducted and generally well tolerated mechanism to measure stress markers. The association with age, even in this narrow age range, likely represents the manifold changes in circumstances (financial independence, becoming parents, increased risk of substance use and mental illness) that occur during this transitional period of life, particularly for young Indigenous women. LAY ABSTRACT Chronic stress can impact negatively on health and emotional wellbeing. A hair sample is an easy way to measure chronic stress in Indigenous and non-Indigenous young people. The markers of chronic stress, cortisol and cortisone, were different between Indigenous and non-Indigenous, men and women and increased with age in Indigenous young adults.