The Mediterranean peninsulas host rich assemblages of lizards, but little is known about the factors that limit their habitat use on large spatial scales. In this study, we investigated the variation in habitat use of 29 species of lacertid lizards on the Iberian and Italian peninsulas and the transitional region of southeastern France. We investigated whether the types of habitat used were phylogenetically determined or, in contrast, were more influenced by spatial or climatic effects. We characterized the vegetal composition of 483 habitats used by lacertids and estimated the contribution of each component to habitat variability using distance‐based redundancy analysis. We showed that overall turnover patterns were determined similarly in both peninsulas, despite differences in the composition of the lacertid assemblages. The aridity‐related component dominated over the phylogenetic one, which has a weak influence in both regions. The species showed different turnover patterns, being low in those present in cold alpine habitats and shrub‐steppe specialists. In some Iberian endemics, habitat turnover occurs within relatively homogeneous climatic bands. However, in the Italian species, habitat turnover has a comparatively stronger climatic component, suggesting lower climatic specialization. This study shows that species distributions across habitats provide information to assess community properties and can be applied to explore differences among faunal assemblages over large geographic areas. Our results provide evidence that beta diversity can play a key role in structuring patterns of habitat turnover.