Body size and morphology are important traits that can strongly influence the life history of an organism. One important factor affecting these traits is habitat. Urbanization has resulted in the significant modification of many habitats, and thus, it may be a factor affecting the body size and morphology of species living in the urban environment. In this study, we compared body size and morphology in urban and bush populations of the lizard Lophognathus temporalis in and around Darwin, Australia. We made monthly measurements of invertebrate abundance and soil moisture during one year to compare seasonal variation in resource availability between habitats. We also collected all matter excreted by L. temporalis during their first four days in captivity as an index of food consumption in the field. We found that male L. temporalis were larger than females and that urban L. temporalis were larger than bush L. temporalis. Males had longer front limbs, hind limbs, and tails than did females; and in urban populations, they also had larger heads. Urban L. temporalis had longer front and hind limbs than did bush L. temporalis, although head size and tail length were similar for both groups. Resource availability was seasonally more stable in urban habitats than in bush habitats, and urban L. temporalis consumed more than bush L. temporalis all year round. We conclude that differences in resource abundance between habitats may be an important factor contributing to the morphological differences between urban and bush-dwelling L. temporalis.