Burrowing mammals impact the physical characteristics of the environment with their activity and, as a result, increase plant and animal biodiversity. The Siberian marmot (Marmota sibirica) is a globally endangered species inhabiting piedmont, mountain steppes, and alpine meadows in Mongolia and neighboring countries. Identifying a standardized national survey protocol in Mongolia is the first important step to developing a science-based management program and specific conservation measures for this endangered species. We used drones to collect aerial images of high-elevation Mongolian steppe grasslands to assess the efficacy of the application of this technology to count and monitor Siberian marmot population trends in a UNESCO Biosphere Reserve, Bogd Khan Mt. Based on the appearance of their entrance, we identified burrows on the ground on images and classified them as active (summer-living, hibernacula) and non-active. The drone survey was more effective in detecting and classifying burrows than ground survey and the detectability of burrows on aerial images taken at 150 m above ground was higher than 0.9. We counted burrows in images acquired by the drone in spring and early summer. Burrows in spring were more easily detectable compared to summer because of the absence of vegetation which made the differences in the color of the ground more pronounced. However, the summer counts were similar to spring. We suggest that seasonal counts might provide different ecological information about the marmot’s habitat and population in space and time. Drone images also allowed the detection of differences in marmot populations between sites. This study represents a first step towards the development of a survey protocol to assess the status of this endangered mammal and for conservation planning aimed at restoring its key functional role in the grassland ecosystem.