In polydomous ants, individuals belonging to a single colony occupy a variable number of neighbouring nests. Polydomy is frequently associated with polygyny and species are often both facultatively polydomous and facultatively polygynous. In this study we test the generality of this association by investigating the genetic and spatial structure of polydomous colonies of Iridomyrmex purpureus in New South Wales, Australia. Genetic analysis of 15 colonies revealed high relatedness within all but one of the colonies, indicating that the workers are mostly produced by one, singly inseminated queen. Polydomy in this population therefore is not associated with polygyny. Intriguingly, our behavioural data suggests that the colony with low within-colony relatedness had been recently formed by colony fusion. While genotypes were not distributed homogenously throughout this newly formed colony, there was an obvious exchange of genotypes between the nests of the two former colonies. During 2 years of field observations in which we observed 140 colonies comprising over 1000 nests, we observed colony fusion only twice. We discuss these findings in relation to the current theories on the relationship between polydomy and polygyny.