Animals that are exposed to environmental stressors may experience chronically elevated glucocorticoid (GC) levels, which can lead to deleterious effects such as immune and reproductive system suppression. Such effects are of special concern in rare species. We measured fecal GC concentrations in endangered San Joaquin kit foxes (Vulpes mocrotis mutica) to assess stress responses in natural and urban habitats. Basal GC levels were significantly higher (P < 0.01) among urban foxes (5.3 ± 2.2 ng cortisol/g dry feces; n = 32) than among foxes in natural habitats (4.7 ± 0.5 ng cortisol/g dry feces; n = 179). In the natural habitat, potential stressors included predation risk, particularly in areas with shrubs where coyote (Canis latrans) abundance was higher. In the urban habitat, the primary stressors were anthropogenic disturbances (e.g., human activity, vehicles). Foxes in natural habitats exhibited acute stress responses when trapped, but exhibited similar mean GC levels between areas of high and low predation risk, suggesting adaptation to the presence of coyotes. Urban foxes did not exhibit acute responses when trapped, suggesting adaptation to the presence of humans. Stress responses based on GC levels indicated that foxes in both natural and urban habitats are habituated to the primary stressors in each habitat, thereby mitigating chronic stress.