An understanding of the relationship between vegetation spatial heterogeneity and disturbance and its application to the management are important for maintaining biodiversity and functions of ecosystems. We examined the effects of disturbance by Siberian marmots on the spatial heterogeneity of vegetation at three spatial scales (fine, intermediate and coarse) in a Mongolian grassland. We established a 50 m x 50 m plot around five marmot mounds and another plot in an area with no mounds. Each plot was subdivided into 625 adjacent 4-m2 square quadrats and the plants in them were surveyed. Spatial heterogeneity was calculated as the mean dissimilarity in species composition among sample quadrats in each plot. The off-colony plant community was dominated by graminoids, but a variety of plants, including graminoids, forbs and shrubs, were present in the on-colony plot. The slightly greater fine-scale heterogeneity in the on-colony plot compared to the off-colony plot reflected the presence of either disturbed or undisturbed patch within a single measurement unit, whereas the lower coarse-scale heterogeneity in the on-colony plot reflected the presence of both disturbed and undisturbed patches within a single measurement unit. Our results demonstrate the possibility of using the marmot as a conservation tool in our study site as far as a plant biodiversity is targeted.