This study examined the effects of a fern-dwelling ant species, Crematogaster difformis Smith (Formicidae, Hymenoptera), which defends territories in large areas of the crowns of emergent trees, on the composition and spatial distribution of other ant species on the trees in a Bornean tropical rainforest. We investigated the within-tree distribution of nest sites and foraging areas of individual ant colonies on emergent trees. The ant species composition on trees occupied by C. difformis was significantly different from that on conspecific trees without C. difformis. The species richness of ants inhabiting emergent trees, colony abundance of ants that nested and foraged in the crowns, and colony abundance of ants that nested on and in the ground but foraged in the crowns were all significantly lower on trees occupied by C. difformis than on conspecific trees without C. difformis. These results suggest that C. difformis suppresses the distribution of other ant species on emergent trees by excluding them from C. difformis territories and that a single ant species can affect the structure of the entire ant assemblage in the canopy of tropical rainforests.