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Context Species distribution is influenced by environmental variables, including biotic and abiotic factors, adaptive capability, and dispersal. This study focused on habitat utilisation patterns of the following three gecko species within Girraween National Park, south-east Queensland: the granite leaf-tailed gecko (Saltuarius wyberba), Lesueur’s velvet gecko (Amalosia lesueurii), and the southern spotted velvet gecko (Oedura tryoni). Aim The aim was to investigate gecko presence, abundance, and substrate use in relation to macro- and microhabitat. Methods In total, 53 spotlight surveys were undertaken across three sites and multiple seasons, focusing on spring and summer. One site was surveyed per night, involving searching for geckos along three defined 150 m transects within the site (1.7 h searching on average) and recording the location, microhabitat, and species of all detected individuals. Microhabitat structure and habitat availability were assessed using standardised plots along the same transects as for the gecko surveys and from satellite imagery. Key results Each gecko species displayed distinct microhabitat associations, but different microhabitats were used at different sites, particularly by S. wyberba. This was influenced, but could not be fully explained, by the differences in microhabitat structure and availability among sites. However, predictably, the site with the greatest habitat heterogeneity (the Valley), which presumably provided additional niches for habitat specialists, supported higher species diversity and abundance. Landscape topography also influenced gecko abundance, with geckos tending to be more clustered in sites with steep landscape features. Gecko presence and abundance may have been influenced by niche partitioning and, although not quantified in this study, the availability of suitable retreat sites. Conclusions This study demonstrated that species-specific responses to microhabitat structure, and not just habitat availability, drive gecko presence and abundance. Patterns of substrate use suggest that even habitat specialists may exhibit local behavioural flexibility in structurally complex environments. Implications This study has provided new information about habitat partitioning dynamics and the influence of habitat heterogeneity and structure on gecko assemblages. It has highlighted the importance of conserving structurally diverse granite environments to support both generalist and specialist reptile species. These findings can inform targeted conservation strategies for habitat-restricted geckos such as Saltuarius wyberba.