The Mongolian marmot (Marmota sibirica) is a relatively large-bodied, social rodent that lives in colonies across the Mongolian steppes and adjacent parts of China and Russia. Marmots serve as ecosystem engineers that display multiple functions on the steppe environments they inhabit. Mongolian marmots experienced a 75% decline across Mongolia in the 1990s that led to their listing as endangered globally. The decline of marmots likely affected other species given their importance to the ecosystems they inhabit. To examine the role of marmots on herpetofauna, we established drift fence arrays with associated pitfall and funnel traps on active marmot colonies, inactive colonies, and control sites in the forest-steppe and semi-desert zones of Mongolia. In total, we identified 555 individuals representing 5 species of reptiles in Ikh Nart Nature Reserve (semi-desert) from 2010 – 2011 and 22 individuals of 3 species of reptiles and one amphibian species in Hustai National Park (forest-steppe) in 2014 and 2016. We found significantly higher species abundance and some diversity indices on active and inactive colonies compared to control sites in Hustai. Vegetation height and cover significantly affected the abundance and species richness of reptiles in Ikh Nart. In Ikh Nart, we found that under conditions of higher vegetation cover and height, reptiles were distributed more widely across the landscape, but with lower vegetation cover and height, reptiles associated more strongly with marmot burrows. Burrows likely provide shelter from extreme climatic conditions and refugia from predation. Our research provides insights into how marmots create important habitats for associated fauna. This and similar experimental approaches will allow us to better understand the biodiversity patterns in and around marmot burrows.