The impact of invasive species on island faunas can be of major local consequence, while their control is an important part of island ecosystem restoration. Among these invasive species are ants, of which some have a disruptive impact on indigenous arthropod populations. Here, we study the impact of the invasive African big-headed ant, Pheidole megacephala, on a small Seychelles island, Cousine, and assess the impact of this ant, and its chemical control, using the commercially available hydramethylnon-based bait, Siege, on the endemic keystone Seychelles giant millipede species, Sechelleptus seychellarum. We found no significant correlations in landscape-scale spatial overlap and abundance between the ant and the millipede. Furthermore, the ant did not attack healthy millipedes, but fed only on dying and dead individuals. The chemical defences of the millipede protected it from ant predation. Ingestion of the bait at standard concentration had no obvious impact on the millipede. The most significant threat to the Seychelles giant millipede in terms of P. megacephala invasion is from possible catastrophic shifts in ecosystem function through ant hemipteran mutualisms which can lead to tree mortality, resulting in alteration of the millipede's habitat.