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Sympatric species can coexist through ecological resource partitioning as for example for habitat, food or time. However, a detailed understanding of the basic thermal physiology, crucial for temporal partitioning, is currently lacking, especially for the desert rodents. Here, we compare the physiological performance with regard to thermal energetics and morphological traits of two sympatric gerbils from the Gobi desert of Inner Mongolia, China. The diurnally active Meriones unguiculatus and the nocturnally active M. meridianus. The diurnal M. unguiculatus had more brown adipose tissue (BAT) mass and capacity for non-shivering thermogenesis (NST), a higher resting metabolic rate (RMR) at low ambient temperatures (T-a) and a higher upper critical temperature of the thermal neutral zone (TNZ) than the nocturnal M. meridianus. The overall thermal conductance and lower critical temperatures of M. unguiculatus were also higher than that of M. meridianus, permitting the former to maintain a stable body temperature (T-b) when exposed to high T-a. Laboratory-bred M. meridianus also showed higher daily water intake. We found no differences in body mass, and total evaporative water loss (TEWL) between the two species captured from the natural environment. These results suggest that the diurnal M. unguiculatus have a higher tolerance of high T(a)s, whereas M. meridianus can save more energy at low T(a)s. Therefore, from the view point of energy conservation, our results suggest that the nocturnal ecophenotype in M. meridianus is constrained by a lower ability for heat resistance, but this is not the case for the diurnal M. unguiculatus.