The lizards Podarcis muralis and Iberolacerta horvathi display an overall similarity in morphology and ecology. Although they are widely sympatric in part of their distribution range of Slovenia, areas of altitudinal segregation have been observed. Ecophysiological traits such as preferred body temperatures (Tp) and rates of evaporative water loss (EWL) are some of the factors likely to be subjacent to this pattern. We expect the species that is more abundant in higher altitudes to have lower Tp and higher EWL (due to lower environmental temperatures at higher elevations) than the species that is more abundant in lowlands. We conducted lab experiments to determine whether intra- and interspecific variation in these two physiological traits exists. Contrary to expectations, the means of Tp were similar between the species, but their seasonal dynamics differed, which indicates that thermal accuracy might be more important. Species differed in seasonal (and daily) variation of Tp, rising from spring to summer more in P. muralis than in I. horvathi. Comparing instantaneous EWL, our results showed interspecific differences with higher values in P. muralis than in I. horvathi. Throughout a 12-h period, the accumulative EWL was also always higher for P. muralis than for I. horvathi, with the greatest differences occurring after 9–12 h of the experiment. Further studies should focus on investigating if these divergent physiological characteristics of both species are associated with their habitat use (in terms of thermal and water environment) and species interaction.