Some species of ants possess an unusual form of social organization in which aggression among nests is absent. This type of social organization, called unicoloniality, has been studied in only a handful of species and its evolutionary origins remain unclear. To date, no study has examined behavioural and genetic patterns at points of contact between the massive supercolonies that characterize unicoloniality. Since interactions at territory boundaries influence the costs of aggression and the likelihood of gene flow, such data may illuminate how supercolonies are formed and maintained. Here we provide field data on intraspecific territoriality for a widespread and invasive unicolonial social insect, the Argentine ant (Linepithema humile). We observed abrupt and well-defined behavioural boundaries at 16 contact zones between three different pairs of supercolonies. We visited nine of these zones weekly during a six-month period and observed consistent and intense intercolony aggression that resulted in variable, but often large, levels of worker mortality. Microsatellite variation along six transects across territory borders showed that FST values were lower within supercolonies (0.08 ± 0.01 (mean ± SE)) than between supercolonies (0.29 ± 0.01) and that this disparity was especially strong right at territory borders, despite direct and prolonged contact between the supercolonies. Matrix correspondence tests confirmed that levels of aggression and genetic differentiation were significantly correlated, but no relationship existed between geographic distance and either intraspecific aggression or genetic differentiation. Patterns of FST variation indicated high levels of gene flow within supercolonies, but little to no gene flow between them. Overall, these findings are inconsistent with a model of relaxed ecological constraints leading to colony fusion and suggest that environmentally derived cues are not the prime determined of nestmate recognition in field populations of Argentine ants.