Habitat structure is a key determinant of variation in biodiversity. The effects of increased vertical and horizontal vegetation structure can result in marked shifts in animal communities. This is particularly true for ants in response to woody thickening, with predicted negative impacts on ant diversity. We used pitfall traps to study the response of epigeic ants in two co-occurring dominant habitats (closed and open) of an African savanna biome experiencing extensive woody thickening. Although species richness was higher in open habitats, evenness was significantly lower. Thickening explained significant amounts of variation in ant composition, but site-specific characteristics and seasonality were more important. These site-specific characteristics were largely linked to Anoplolepis custodiens, a species that were locally abundant in open habitats with clayey soils, where they often accounted for more than 90% of all ant activity. As A. custodiens also responds positively to disturbance, indiscriminate bush clearing could lead to knock on effects associated with the numerical and behavioural dominance of this species.