Abstract Many species are declining due to environmental and physical changes in their habitats. Such disturbs alter the availability of micro-habitats and influences the presence of lizards, being even worse for threatened and endemic species. Glaucomastix littoralis is a teiid species restricted to four restingas areas of Brazil. The understanding about the use and preferences of micro-habitats by the species and the consequents effects of substrate loss is important to prevent local extinctions. This study took place in restingas of Maricá, Jurubatiba and Grussaí, in Rio de Janeiro State. We sampled the vegetation of all areas, to access differences between the physical structures, and recorded the individuals sighted and the micro-habitat they were in, to investigate the relation of individuals and habitat structure. We calculated the frequency utilization of each micro-habitat and made a presence estimation of individuals (occupancy and detection probability) to assess which structural parameters of vegetation guide the settlement of the studied populations. Our data showed structural vegetation particularities among the areas and a trend concerning the use of micro-habitat by Glaucomastix littoralis, with a general preference for leaf litter inside bushes, guriri and bare sand and a low utilization of cactus and herbaceous. We also found positives (bare sand and cactus) and negatives (bushes) influences of micro-habitats in relation to the occupation of the areas by the individuals. Since vegetation is fundamental to lizards, due to their use as a refuge, site for thermoregulation and feeding, the understanding about the effects habitat degradation/fragmentation can cause is essential to create appropriate management plans and develop public policies to conserve the species.