We investigated the structure of a lizard assemblage from Seasonally Dry Tropical Forest enclaves in the Brazilian Cerrado biome, by testing the roles of ecological and historical components. We analysed data from 469 individuals, belonging to 18 lizard species, sampled by a combination of pitfall, funnel and glue traps, as well as by haphazard sampling. Null model analyses and Canonical Phylogenetic Ordination analysis, coupled with Monte Carlo simulations, revealed lack of both ecological and phylogenetic structure in microhabitat use. Conversely, these analyses revealed a mean overlap in diet composition significantly smaller than expected by chance and significant historical structure. Structure in diet composition was due to phylogenetic effects corresponding to the most basal divergence of the squamate phylogeny (Iguania/Scleroglossa) and the clades Teiidae and Gymnophthalmidae. Among lizards, evolutionary constraints on microhabitat use appear less than on prey use, suggesting that the availability of historically preferred prey types moderates microhabitat selection. The lack of structure in microhabitat use suggests absence of competitive interactions on the spatial component. On the other hand, food preferences have a deep historical basis and do not reflect current competitive interactions.