We used null model analyses to investigate the existence of structure in lizard assemblages from open vegetation enclaves in Rondônia, southwestern Amazonia, in relation to species richness, species co-occurrence, diet, and size overlap. These enclaves presumably have been isolated since the Holocene, providing a history of long-term isolation. We assumed that the presence of structure in lizard assemblages from the Rondônia enclaves is consistent with the notion that extinctions are a deterministic process, some species being more prone to extinction than others. We grouped enclaves into four categories: latosoil cerrado, sandy cerrado, transitional forest, and rocky field. We collected 14 Cerrado lizard species, consisting of five families in all sampled areas. Analyses of species richness, co-occurrence, diet overlap, and size overlap patterns suggested lack of organization in the assemblages. The assemblages from the rocky fields of Guajará–Mirim and the sandy cerrados in Vilhena were significantly structured in diet overlap, whereas the remaining assemblages lacked structure. This probably resulted from phylogenetic inertia and not from ecological interactions. Our results suggest that extinctions proceeded in a stochastic fashion and that historical factors had a dominant role in shaping lizard assemblages in detriment of present-day ecological factors. In addition, we identified endemic species in the enclaves as well as a tight association between unique ecogeographic features of the landscape and species occurrences. We propose that conservation measures in the region must adequately preserve these features to ensure the survival of the species.