Social insects, ants in particular, show considerable variation in queen number and mating frequency resulting in a wide range of social structures. The dynamics of reproductive conflicts in insect societies are directly connected to the colony kin structure, thus, the study of relatedness patterns is essential in order to understand the evolutionary resolution of these conflicts. We studied colony kin structure and mating frequencies in two closely related Neotropical ant species Pachycondyla inversa and Pachycondyla villosa. These represent interesting model systems because queens found new colonies cooperatively but, unlike many other ant species, they may still co-exist when the colony becomes mature (primary polygyny). By using five specific and highly variable microsatellite markers, we show that in both species queens usually mate with two or more males and that cofounding queens are always unrelated. Polygynous and polyandrous colonies are characterized by a high genetic diversity, with a mean relatedness coefficient among worker nestmates of 0.27 (± 0.03 SE) for P. inversa and 0.31 (± 0.05 SE) for P. villosa. However, relatedness among workers of the same matriline is high (0.60 ± 0.03 in P. inversa, 0.62 ± 0.08 in P. villosa) since males that mated with the same queen are on average closely related. Hence, we have found a new taxon in social Hymenoptera with high queen-mating frequencies and with intriguing mating and dispersal patterns of the sexuals.