Coleodactylus natalensis is endemic to Atlantic Forest fragments in Rio Grande do Norte state, coastal northeastern Brazil. The main fragment where the species lives is the Parque Estadual Dunas de Natal “Jornalista Luiz Maria Alves”, a Conservation Unit covered predominantly by dunes and surrounded by urban areas. Because of the vulnerability of this species and the importance of the PEDN, we studied the density, spatial distribution and habitat and microhabitat preferences of this population to provide basis for future conservation efforts. We randomly sampled ninety-six 50 m² quadrats in each of the four habitats identified in the study area, finding a mean density of 98.5 ± 75.5 lizards per ha^-1, with grouped distribution in the forested habitats and random in others. The species preferentially inhabits the leaf litter of forest habitats at lower elevations, in wetter places and milder temperatures than the mean of our study area. Due to the relatively small density when compared to other Sphaerodactylidae, restricted distribution to forested habitats, and the urban expansion that puts the northeastern Atlantic Forest at constant risk, it is imperative to take conservation measures for this population of C. natalensis.