We compared sexual dimorphism of body and head traits from adult lizards of populations of Gallotia caesaris living in ecologically different habitats of El Hierro and La Gomera. Males had larger body sizes than females, and sexual size and shape dimorphisms were greater in a population from La Gomera than in three populations from El Hierro. Multivariate analyses of variance, using linear and shape-adjusted traits, showed that the populations differed significantly in body and head traits, with pileus (head) width, snout–vent length (SVL), and body mass the main traits contributing to the differences. Males had larger SVL, heads, and limbs than females in all populations, but SVL relative to a shape index (calculated as the geometric mean of several body parameters) was larger in females than in males. Moreover, shape-adjusted hind-limb lengths were significantly shorter in lizards from the more densely vegetated habitats than in those from the less vegetated ones. The magnitude of sexual dimorphism was larger for relative limb length and head depth in the populations with less vegetation than in those with more vegetation. Our data suggest that morphological differences between populations reflect local adaptation to habitat structure.