Habitat management can generate variation in a cascade of organismal traits linked to the environment, particularly in small, endemic species such as the Florida scrub lizard (Sceloporus woodi). For example, reduction of arboreal perches through clear-cutting in managed Florida scrub may alter lizard behavior, and predation risk, which in turn, may alter lizard abundance. We ask whether risk aversion behavior is habitat-specific, and potentially reflects predation intensity. Four predator avoidance traits were quantified in S. woodi from longleaf pine and Florida scrub habitats. We also asked if habitat type was linked to phenotypic traits (e.g., body size, hind limb length) that might alter risk aversion behaviors. Lizards in longleaf pine had greater detection distance and flight distance and were farther from refuges, indicating higher risk aversion compared to populations in Florida scrub. Given this, males may be more sensitive to predation than females, especially during the breeding season. Males were encountered more often than females in both habitats, and detected from a greater distance in longleaf, but not Florida scrub. Population density may affect lizard behavior, yet we found no difference in population density between the habitats for stands sampled, nor any relationship of population density to risk aversion behaviors. These results demonstrate that management activities, which alter vegetation and substrate characteristics, also alter aspects of lizard behavior that subsequently may influence predation pressure among sub-populations.