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The greenhead ant Rhytidoponera metallica has long been recognized as posing a potential challenge to kin selection theory, because it has large queenless colonies where apparently many of the morphological workers are mated and reproducing. However, this species has never been studied genetically and important elements of its breeding system and kin structure remain uncertain. We used microsatellite markers to measure the relatedness among nestmates, unravel the fine-scale population genetic structure, and infer the breeding system of R. metallica. The genetic relatedness among worker nestmates is very low but significantly greater than zero (r = 0.082 ± 0.015), which demonstrates that nests contain many distantly related breeders. The inbreeding coefficient is very close to and not significantly different from zero, indicating random mating and lack of microgeographic genetic differentiation. On average, closely located nests are not more similar genetically than distant nests, which is surprising, as new colonies form by budding and female dispersal is restricted. Lack of inbreeding and absence of population viscosity indicates high gene flow mediated by males. Overall, the genetic pattern detected in R. metallica suggests that a high number of moderately related workers mate with unrelated males from distant nests. This breeding system results in the lowest relatedness among nestmates reported for social insect species where breeders and helpers are not morphologically differentiated.