Species' tolerance of and response to fire varies. Environments that experience frequent fires will contain fire-tolerant fauna, whereas fauna that occur in environments that burn infrequently may lack strategies to cope with fire. In 2003, intense summer wildfires in southeastern Australia's alpine region burned more than 1.3 million ha. The Guthega Skink, Liopholis guthega, is an endangered lizard that is restricted to two geographically isolated alpine locations affected by these fires: Kosciuszko National Park in New South Wales, and the Bogong High Plains in Victoria. We investigated the long-term effects of fire on L. guthega populations through surveys of burned and unburned habitat on the Bogong High Plains. We found L. guthega selected specific microhabitats that are restricted on the Bogong High Plains. Their selection of less-vegetated microhabitats suggests that they may favor an early successional environment. We found retreat site selection differed between sites; at burned sites L. guthega burrowed preferentially under rocks, and at unburned sites comparatively more burrows were positioned at the base of shrubs. Our results suggest that in this species' Victorian range they may be more tolerant to fire than previously thought, likely because of the protection afforded by their burrows. However, our surveys of L. guthega populations from past records also suggest potential local extinctions. To determine the immediate and longer-term effects of intense fires on threatened species, it is important to have prefire data on species and prompt postfire assessments to obtain results applicable to management.