Colony breeding systems and dispersal strategies of eusocial insects shape the genetic structure at the colony, but also at the population level. Most of the few molecular studies dedicated to termites suggest that winged reproductives disperse far enough to secure the formation of outbred founding pairs. However, these studies almost exclusively focused on wood-feeding termites and knowledge about the dispersal potential of winged reproductives is missing for soil-feeding termites. We investigated the dispersal and mating strategies of Embiratermes neotenicus and Silvestritermes minutus (Termitidae, Syntermitinae), two very abundant soil-feeding species from the Neotropics. In both species, analysis of microsatellite markers indicated low genetic similarity between closely located colonies and low genetic differentiation between populations separated by less than 10 km. Each of the 39 E. neotenicus colonies originated from a single pair of primary reproductives and the mean inbreeding coefficient of sterile castes was only slightly different from that expected in offspring of an outbred pair. Most S. minutus colonies (34/41) were consistent with outbred biparental foundation. In three mature colonies, the genotypes of sterile castes suggested their origin by mixing of multiple related reproductives. Finally, four colonies in late stage of the colony life cycle contained sterile populations originating from multiple unrelated reproductives. We conclude that long-distance flights resulting in outbred reproduction are common in these soil-feeding species in pristine habitats but that other factors, such as mating preferences, could increase relatedness between founders.