Animals that are successful in urban habitats often have reduced antipredator responses toward people (sometimes called “fear” responses). However, few studies test whether sympatric species differ in their responses to humans, which may explain differing sensitivities to urbanization. Here, we quantified the behavioral and physiological responses to humans in two lizard species, side-blotched lizards (Uta stansburiana) and western fence lizards (Sceloporus occidentalis), across three different habitat types that vary in human impact: natural habitats with low levels of human activity, natural habitats with high levels of human activity, and urban habitats. We found that side-blotched lizards had longer flight initiation distances, were found closer to a refuge, and were more likely to hide than fence lizards, behaviors that could indicate greater fearfulness. Both lizard species were found closer to a refuge and were also more likely to hide in the urban habitat than in the natural habitat with low human impact, which could represent adaptive behaviors for increased risks in urban areas (e.g. cats). Western fence lizards exhibited lower body sizes and conditions in the habitats with moderate and high levels of human activity, whereas these traits did not differ among habitats in side-blotched lizards. Baseline and stress-induced corticosterone concentrations did not differ across habitats for both species, suggesting that human-impacted habitats were not stressful or that lizards had undergone habituation-like processes in these habitats. Taken together, our results highlight the importance of standardized measurements across multiple species in the same habitats to understand differential responses to human-induced environmental change.