Since the 1987 federal listing as threatened of western populations of gopher tortoises (Gopherus polyphemus), tortoise population recovery and habitat restoration efforts have been implemented at Camp Shelby Joint Forces Training Center, Mississippi. We studied plant community and edaphic features around tortoise burrows and at non-occupied locations in 2007. We investigated relationships between burrow presence and habitat characteristics through decision tree and logistic regression analyses. Burrow occurrence was positively related to stem counts of woody plants and species richness of native legumes and negatively related to overstory canopy coverage and maximum tree height. Cross-validation procedures predicted presence of burrows for 91% of observed outcomes. Tortoise burrows were most often found on side slopes of sand ridges where overstory canopy coverage was <60% and conditions were adequate for burrowing, nesting, basking, and establishment of food plants. Our study sites exhibited woody plant coverage >45% at ground and midstory levels and <50% coverage of herbaceous plants. Advancement of these conditions over time can produce suboptimal habitat quality yet tortoises may continue to utilize home burrows due to burrow site fidelity, interspersion of desirable food plants, and suitable soils for burrowing. Advancing shrub and sapling cover on our study sites were potentially related to reduced fire return intervals and burning bans associated with forest damage from the 2005 landfall of Hurricane Katrina. Design and interpretation of tortoise habitat studies should consider many factors, including edaphic and vegetation conditions, history of habitat management, temporal effects on vegetation succession, activity status of burrow, and burrow site fidelity.