Liolaemus is a species-rich genus endemic to South America with relatively little known about the biology of most of the > 200 included species. One species, L. silvai is common in the coastal Atacama Desert and is sexually dimorphic. We studied their phenotypic variation in color and body size, as well as habitat use by capturing lizards active on the surface. To assess phenotypic variation, we categorized the color morph of each lizard based on visible coloration in their ventral throat region and their ventral body from the shoulder girdle to the hips. We also sexed each lizard, measured snout–vent length and body mass, and recorded incidences of tail breakage. For habitat use we measured perch height, distance from the rock edge to nearest vegetation, and the height of the rocks on which lizards were initially sighted. We assessed habitat selection by comparing perch characteristics to features available in the habitat by pairing capture rocks with the nearest rock in a random direction from the initial perch site. Male L. silvai were significantly larger than females, but color morph and tail break frequency were independent of sex. Lizards used rocks that were significantly closer to vegetation than random rocks available in the environment independently of sex or color morph. We document the same pattern for perch height. Future studies are needed to examine the exact role of vegetation for L. silvai.