The Bolson tortoise, Gopherus flavomarginatus, occurs within a restricted geographical area in the Mexican Chihuahuan Desert. We analyzed the variation in surface microhabitat with relation to the burrow occupancy for this tortoise at the Mapimí Biosphere Reserve, Mexico. In summer 2010, we monitored burrow activity (active, inactive, or abandoned) and measured environmental factors that might influence the burrow’s occupancy by tortoises (air temperature, relative humidity and substrate temperature, both inside and outside the burrow, and the plant cover around it). Discriminant analysis was used to identify the importance of these variables influencing burrow occupancy. Correlation and linear regression analyses were performed to quantify the relation between environmental factors in the sampled burrows. Results. Sixty-one burrows were identified at the Tortugas locality. The first function’s auto-value analysis indicates that this function explains 97.9% of the variation in burrow activity status; high occupancy scores were associated with low substrate temperature inside the burrow. Plant cover was inversely proportional to substrate temperature inside the burrow. These results suggest the importance the density of plants surrounding the tortoise’s burrow as a key factor influencing the burrow microclimate and occupancy by the tortoises. Conclusions. Gopherus flavomarginatus inhabits burrows, in part, based on microhabitat structure, with plant cover being a main factor influencing burrow occupancy. Our findings indicate that human land use and vegetation management are important for conserving Bolson tortoises, and for understanding habitat conditions necessary for the successful establishment of populations elsewhere.