If community structure is influenced by habitat structure at a local level, then it should be possible to tie species occurrence to key habitat variables. We used a pitfall-trap system to determine the relationship of species composition, species diversity (relative abundance), and community structure to habitat structure along a transect through a habitat gradient in the Brazilian Cerrado. A total of 531 individuals of 12 lizard species were sampled. A species accumulation curve based on EstimateS and a curve-fitting protocol predicted 12 species at day 22 and all species by about day 40. We registered 12 species at day 11. Trapping success declined through time, likely because of a combination of removal along the transect and seasonal environmental change (wet to dry). The more open end of our transect experienced higher temperatures in all microhabitats sampled, suggesting thermal structure associated with vegetative structure. A Canonical Correspondence Analysis showed that lizard species composition and relative abundance respond to variation in vegetative and physical structure of the habitat at small scales. Consequently, maintenance of habitat gradients should be considered in programs aimed at maintaining local biodiversity.