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Throughout the tropics, agroforests are often the only remaining habitat with a considerable tree cover. Agroforestry systems can support high numbers of species and are therefore frequently heralded as the future for tropical biodiversity conservation. However, anthropogenic habitat modification can facilitate species invasions that may suppress native fauna. We compared the ant fauna of lower canopy trees in natural rainforest sites with that of cacao trees in agroforests in Central Sulawesi, Indonesia in order to assess the effects of agroforestry on occurrence of the Yellow Crazy Ant Anoplolepis gracilipes, a common invasive species in the area, and its effects on overall ant richness. The agroforests differed in the type of shade-tree composition, tree density, canopy cover, and distance to the village. On average, 43% of the species in agroforests also occurred in the lower canopy of nearby primary forest and the number of forest ant species that occurred on cacao trees was not related to agroforestry characteristics. However, A. gracilipes was the most common non-forest ant species, and forest ant richness decreased significantly with the presence of this species. Our results indicate that agroforestry may have promoted the occurrence of A. gracilipes, possibly because tree management in agroforests negatively affects ant species that depend on trees for nesting and foraging, whereas A. gracilipes is a generalist when it comes to nesting sites and food preference. Thus, agroforestry management that includes the thinning of tree stands can facilitate ant invasions, thereby threatening the potential of cultivated land for the conservation of tropical ant diversity.