Invasive species are one of the main reasons for the ongoing global loss of biodiversity. Anoplolepis gracilipes is an invasive ant that has recently received significant attention due to its negative effect on the native fauna and flora of Christmas Island, Indian Ocean. This species has contributed to a drastic change in the structure of the Christmas Island rainforest through its negative impact on the island s endemic red land crab, the dominant consumer on the islands forest floor. In this study, we investigate the population structure of A. gracilipes on Christmas Island in order to determine whether multiple introductions occurred on the island and how they correspond to known infestations. We genotyped 578 individuals collected from 50 nests across the Island. We identify two distinct subgroups in the population that represent two different supercolonies. These supercolonies are interspersed across the island, however both nuclear (microsatellites) and mitochondrial markers strongly suggest that there is no gene flow between the two colonies. Significant heterozygote excess within the entire sampling area, with all but one worker examined being heterozygous for all seven microsatellite loci, suggests an unusual reproductive system in these ants. Our results are consistent with recent sociogenetic findings in a population of A. gracilipes in Northern Borneo.