Pocket gophers (Geomyidae) require soils amenable to burrowing and vegetation communities that provide adequate foods. We examined the interplay of soil texture and vegetation structure in determining site occupancy of the southeastern pocket gopher (Geomys pinetis), a species of conservation concern throughout its range. Using a case-control sampling design, we compared vegetation structure and soil texture between occupied and unoccupied sites in southeastern Alabama. All occupied sites had soil clay content ≤8.05% at 0–20 cm depth. In logistic regression modeling, clay content had overwhelming support as the most important single habitat variable distinguishing occupied from unoccupied sites. Based on soil results, we focused our examination of vegetation structure on the subset of our sites with <10% clay at 0–20 cm depth. Relative odds of occupancy were highest at intermediate levels of canopy cover; however, canopy cover at occupied sites ranged widely. Compared to unoccupied sites, occupied sites contained less midstory cover and greater ground cover of graminoids and shrubs. Our results demonstrate that although vegetation structure is important in determining site suitability, soil texture may be an overriding constraint limiting potential habitat for this species. Conservation actions for southeastern pocket gophers such as habitat restoration and population translocations should ensure that target sites have suitable low-clay soils.