Pogonomyrmex rugosus and Messor pergandei are ecologically similar species of desert seed-harvester ants that coexist in numerous areas throughout the Sonoran and Mohave Deserts. However, these two species also commonly segregate along physical gradients, with each species predominating in areas that differ in soil texture and/or topographic relief. Along gradients that included bajada and alluvial flat habitats, P. rugosus occurred alone in coarse-textured soils near mountains, while M. pergandei occured alone in finer-textured soils further away. Conversely, along a vegetation gradient that included creosote bush and saltbush habitats, P. rugosus occurred alone in finer-textured soils than those occupied by either M. pergandei alone or both species in coexistence. However, in both situations clay content was significantly higher in areas occupied by P. rugosus alone, and at the latter site clay content was correlated with relative abundance of each species. Moreover, local distribution pattern of these two species may be related to the effects of clay on water retention, with retention being highest in areas occupied by P. rugosus alone. Differences in reproductive ecology may also affect these patterns as P. rugosus reproductive flights follow summer monsoon rains, while those of M. pergandei occur during the milder winter and spring.