Although broad habitat preferences are known for many species of conservation concern, identification of key microhabitat elements critical to persistence and reproduction is a crucial and generally understudied aspect in conservation. In this study, we examined diurnal microsite selection in the five-lined skink (Eumeces fasciatus) to identify important microhabitat elements in its most northerly populations. Seven populations distributed across the southern edge of the Canadian Shield were sampled. To determine which microhabitat elements are important in diurnal microsite selection, ten microhabitat features were compared in occupied and unoccupied quadrats. A Classification and Regression Tree analysis showed that the best predictor of E. fasciatus presence in a meter-by-meter quadrat was proportion of cover rock. This finding will help in modeling or identifying potential historical, current or future habitat in these most northern E. fasciatus populations, and aid population managers in monitoring the habitat suitability of extant five-lined skink populations.