In this study we measured two physiological traits (levels of corticosterone and immunoglobulin) in two species of landbirds, the Canyon Towhee (Melozone fusca) and Inca Dove (Columbina inca), occupying three degrees of human alteration of a subtropical mountain landscape: forest edges, croplands, and urban sites. We found that both physiological variables differed by species and habitat condition. In both species, corticosterone concentration was significantly higher in croplands. But immunoglobulin concentration behaved differently, in C. inca being highest at urban sites, where in M. fusca it was lowest. Contrary to expectation, we only found one strong significant relationship between both physiological variables: M. fusca in urban areas. Our results suggest that 30% of the towhees captured in urban areas are under chronic stress. Results for body condition support this hypothesis, as the condition of towhees in urban areas was poorer, suggesting physiological vulnerability. Although we expected the density of both species to be high in urban areas because of the amount and predictability of resources, we found a significantly lower density of M. fusca in urban areas, suggesting that the habitat variables influencing the physiological condition of M. fusca affected its population density. In summary, our results suggest that a substantial proportion of Canyon Towhees in the urban area studied have physiological limitations, while the Inca Dove seems to have an appropriate physiological response despite low values for body condition in urban areas.