The niche axes of microhabitat use, activity and size for 21 skink species from five assemblages (Alligator Creek, Cairns, Chillagoe, Cooktown and Mt Bartle Frere) in the biodiverse tropics of north-east Queensland were examined. Species within the same assemblage separated predominantly along two structural microhabitat gradients; one that ranged from microhabitats dominated by large rocks to leaf litter and total ground cover, and a second defined by increasing leaf litter, ground cover, undergrowth, proximity to vegetation and increased canopy cover. All species used available microhabitats non-randomly, with species from the same ecotype (arboreal, generalist, litter-dwelling, rock-using) clustering in multivariate ecological space. Despite evidence of within-assemblage niche overlap, null-model comparisons revealed that only one assemblage (Chillagoe) had greater niche overlap than would be expected by chance. Assemblages with more species occupied smaller niche space, indicating species packing. However, species with more diverse niches were less evenly packed. While most species overlapped in activity time and body size, differences among species from the same ecotype were observed. Despite subtle differences in temporal activity and body size, differences in structural microhabitat use appears to be the dominant niche axis allowing the coexistence of species within these assemblages of tropical skinks.