Identifying microhabitat preferences is important in understanding distributions of organisms and crucial to focusing conservation efforts. The Five-Lined Skink (Eumeces fasciatus) is a rock-dwelling diurnal lizard that, in Canada, is considered a species of “special concern” under the recently passed Species at Risk Act (SARA). In this study, we examined the early-season diurnal retreat site selection preferences of the Five-Lined Skink at the northern limit of its range. To determine preferences we compared dimensions, thermal properties, and other associated microhabitat characteristics of rocks under which skinks were found to randomly selected rocks in two populations. A matched-pairs logistic regression revealed that individuals of E. fasciatus prefer longer than average cover rocks located in areas with few trees. We also found that, compared to other available cover element-substrate combinations, rocks lying on a bedrock substrate afford the best opportunities for skinks to achieve preferred body temperatures. These retreat site preferences are likely driven both by the necessities of thermoregulation and protection from predators.