Colony and population genetic structure was determined for Reticulitermes flavipes (Kollar) and Reticulitermes virginicus (Banks) collected from Sentricon Termite Colony Elimination System monitoring stations at an apartment complex in Raleigh, NC. Once in each of 2000, 2001, and 2002, samples of termites were collected from monitoring stations just before the installation of bait tubes containing 0.5% hexaflumuron. Twenty workers from each sample were genotyped at five microsatellite loci. Comparison of worker genotypes among samples provided unambiguous colony associations. Analysis of worker genotypes within colonies coupled with estimates of F-statistics and nestmate relatedness showed that three fourths (30) of the 41 R. flavipes colonies and all three of the R. virginicus colonies were simple families headed by pairs of outbred monogamous reproductives. The remaining R. flavipes colonies were extended families, apparently headed by a few neotenic reproductives. Most colonies appeared to be localized, occupying only a single monitoring station. Termite pressure was initially heavy, with up to five colonies present around a single building simultaneously, but it progressively decreased over time. Of 35 R. flavipes colonies and 1 R. virginicus colony baited in 2000 or 2001, only a single R. flavipes colony was found again 1 yr later, but this colony was not detected the following year. These results suggest that although treatment with hexaflumuron bait successfully suppresses or eliminates Reticulitermes spp. colonies, new colonies can quickly move into areas vacated by treated colonies, but over time continuous baiting can reduce termite pressure and effectively protect structures.