Context Large portions of the world's forests and woodlands are currently affected by declines in canopy condition of dominant tree species; however, the effects of these declines on faunal communities are largely unknown. Eucalyptus wandoo woodlands in the south-west region of Western Australia have demonstrated declines in condition since the early 1990s. Such declines in tree condition can result in reduced understorey vegetation, increased leaf-litter cover and coarse woody debris, potentially altering the habitat and resource available to reptiles. Prescribed fire events, another mechanism of habitat change for reptiles, are a common occurrence in these woodlands. Aims The present research investigated whether reptile communities were influenced by E. wandoo tree condition, and the changes in the habitat associated with E. wandoo decline. Methods Reptile trapping was conducted at 24 E. wandoo-dominated sites (of varying condition) in Dryandra State Forest and Wandoo Conservation Park, Western Australia. Overall, reptile abundance, species richness and individual reptile species abundances (only those species captured in sufficient numbers for analysis) were compared with a range of habitat characteristics that are likely to be altered by changes in E. wandoo tree condition. Key results Overall, higher reptile abundance and species richness were observed at sites with longer time since fire and more site litter cover. There was also a greater abundance and diversity of reptiles at sites where E. wandoo trees exhibited fewer symptoms of tree decline. Similar analyses for the five most common skink species indicated species-specific relationships with tree-condition measures, time since last fire, site litter cover, distance to drift fence from E. wandoo trees, understorey vegetation density and the density of coarse woody debris. Conclusions Abundance and species diversity of the reptile communities in E. wandoo woodlands were strongly related to time since last fire, E. wandoo tree condition and habitat characteristics such as site litter cover and the density of coarse woody debris. Implications Decline in the condition of E. wandoo trees and the fire events in E. wandoo woodlands are both mechanisms of change correlated with reptile habitat and resources. Future management of E. wandoo woodlands may include reducing prescribed fire events in areas demonstrating symptoms of tree decline, to conserve reptile abundance and species richness. © CSIRO 2013.