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Desert hamsters (Phodopus roborovskii) are the least known species in the genus Phodopus with respect to ecology and physiology, and deserve scientific attention, particularly because of their small body size. Here, the responses of energy metabolism and reproductive function to short photoperiods in desert hamsters were investigated. Male and female desert hamsters were acclimated to either long day (LD) (L:D 16:8 h) or short day (SD) photoperiods (L:D 8:16 h) for three months, and then the females were transferred back to an LD photoperiod for a further five months, while at the end of the SD acclimation the males were killed and measurements were taken for serum leptin as well as molecular markers for thermogenesis. We found that like the other two species from the genus Phodopus, the desert hamsters under SD decreased body mass, increased adaptive thermogenesis as indicated by elevated mitochondrial protein content and uncoupling protein-1 content in brown adipose tissue, and suppressed reproduction compared to those under LD. However, different from the other two species, desert hamsters did not show any differences in energy intake or serum leptin concentration between LD and SD. These data suggest that different species from the same genus respond in different ways to the environmental signals, and the desert adapted species are not as sensitive to change in photoperiod as the other two species.