In ectotherms, variation in body temperature (Tb) affects physiological performance and, ultimately, fitness. Therefore, reptiles regulate Tb behaviourally by choosing habitats of optimal temperature. The main goal of this study was to determine the link between patterns of thermoregulation and habitat selection in Common Musk Turtles inhabiting a thermally challenging region. We expected habitat selection to be based on the fulfillment of thermoregulatory requirements, which can be accomplished by selecting thermally superior habitats. From early May to late August 2007, we tracked 22 Common Musk Turtles with temperature-sensitive radio-transmitters and collected daily Tb profiles with automated radio-telemetry data loggers. In addition, temperature data loggers were placed in the study area to measure the range of environmental operative temperatures (Te) available to musk turtles. The habitats with the highest thermal quality were aquatic habitats with surface cover (i.e., lily pads, macrophytes, etc.) followed by shallow water. As expected, musk turtles used habitats non-randomly and had a strong preference for thermally superior habitats. This is consistent with the typical aquatic basking behaviour observed in musk turtles, suggesting that there is a strong link between thermal quality of habitats and habitat selection, even in this almost entirely aquatic turtle.