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Peatlands contain large amount of carbon stock that is vulnerable to release into the atmosphere. Mostly because of human impact, the peatlands at Zoige Wetlands face severe degradation, and the groundwater table is now lower than before, which has increased the population of the plateau zokor, a burrowing rodent. However, the impact of these changes on ecosystem carbon flows has not been studied. To investigate how the plateau zokor and the groundwater level alter the ecosystem respiration of the Zoige peatlands, we sampled the CO2 flux of hummocks shaped by the zokors and compared it with the CO2 flux of undisturbed sites with different groundwater table levels. The soil organic carbon (SOC), soil water content (SWC) and soil temperature at 5 cm (T5) were measured. SOC showed no significant difference among the four sampling sites and did not correlate with the CO2 flux, while SWC was found to partly determine the CO2 flux. A linear equation could adequately describe the relationship between the natural logarithm of the ecosystem respiration and the soil temperature. It is demonstrated that descending groundwater table might accelerate ecosystem respiration and the CO2 flux from hummocks was higher than the CO2 flux from the control site in the non-growing season. With rising temperature, the CO2 flux from the control site accelerated faster than that from the hummocks. Our results show that ecosystem respiration was significantly lower from hummocks than at the control site in the growing season. The results on the impact of zokors on greenhouse gas emissions presented in this paper provide a useful reference to help properly manage not only this, but other litter-burrowing mammals at peatland sites. [ABSTRACT FROM AUTHOR]