The importance of temperature for the biology and ecology of reptiles is well known. In temperate regions where temperatures fluctuate on a daily and seasonal basis, reptiles must respond appropriately to maintain body temperatures that enable activity. In this study, we describe temporal changes in the thermal environment from January to December in Montenegro and the impact on two species of reptile, Hermann’s tortoise, Testudo hermanni, and the large, legless lizard Pseudopus apodus. These reptiles differ in morphology and diet and have a long phylogenetic separation but experience the same thermal environment. To give insight into any impact of these factors on their thermal ecology we calculated monthly thermoregulatory efficiency indexes derived from field body temperatures, set point temperatures—defined as the preferred body temperatures, and temperatures of null models. The results indicated that both species exhibited high thermoregulatory efficiency, with T. hermanni showing the highest levels across the active year and also maintaining higher body temperatures than P. apodus potentially reflecting the dietary and lifestyle differences. During the hottest months, body temperatures of T. hermanni frequently exceeded the set point range but were not exceeded by P. apodus at any time. Microhabitat patches of closely situated sunlight and shaded areas were the most frequently selected patches in both species, with T. hermanni spending greater amounts of time in shaded patches compared to P. apodus. The efficiency indexes, together with data on microhabitat selection, indicated both species moved non-randomly through the environment, selecting appropriate habitat patches and maintaining body temperatures close to the set point range whilst avoiding the dangerously high body temperatures that occur during the hotter months. During the winter months from November to February, the second and third quartiles of the model temperatures fell below the set point range temperatures of both species. This corresponded with their dormant period. In general, the results emphasise the importance of habitat diversity and integrity in reptile ecology and for their conservation.