Species that occur in variable environments often exhibit morphological and behavioral traits that are specific to local habitats. Because the ability to move effectively is closely associated with structural habitat, locomotor traits may be particularly sensitive to fine-scale habitat differences. Anolis lizards provide an excellent opportunity to study the relationship between locomotion and natural perch use in the field, as laboratory studies have demonstrated that lizards that use broader perches develop longer limbs and have higher sprint speeds. We examined Anolis carolinensis (the green anole) in three habitats in close proximity. Our goals were to determine whether habitat-specific differences in hindlimb and toe morphologies occurred in a population in which perch size was variable but not manipulated, whether locomotor behaviors were associated with these morphologies, and whether habitat-specific traits differed between the sexes. We found that while juveniles in the three habitats did not differ in limb or toe morphology, adult females using broader perches had relatively longer limbs than females using narrower perches. Females also differed in toe length across habitats, but not in relation to perch diameter. Males, in contrast, exhibited differing growth patterns (allometry) in these traits, and marginal differences in locomotor behavior. Together, these results suggest that sex-specific responses in morphology and behavior, consistent with experimental observations of phenotypic plasticity, provide a mechanism for refining local habitat use.