The Formosan subterranean termite, Coptotermes formosanus Shiraki, is a major invasive pest species in many parts of the world. We compared the colony breeding system and population genetic structure in three introduced populations in the continental United States: Charleston, SC; City Park, New Orleans, LA; and Rutherford County, NC. Based on worker genotypes at 12 microsatellite loci, we found that colonies were mainly genetically distinct entities consisting of either simple families headed by monogamous pairs of reproductives or extended families containing multiple neotenic (replacement) reproductives descended from simple families. Populations varied from 48% simple families in Charleston to 82% simple families in City Park. Extended family colonies in all three populations were likely headed by <10 neotenic reproductives. There was no significant isolation by distance in any of the populations, suggesting that colonies reproduce by relatively long-range mating flights and/or human-mediated dispersal within each population. The Charleston population showed evidence of a recent genetic bottleneck and most likely was founded by very few colonies. Cluster analysis indicated that the Charleston and City Park populations are quite genetically distant from each other and most likely originated from different source populations. The more recently introduced Rutherford County population was genetically most similar to City Park. These findings, together with results from other infested sites, indicate considerable variation in the genetic structure and breeding system of introduced populations of this species, making it unlikely that there is a simple genetic or behavioral explanation for the success of C. formosanus as an invasive species.