Spread of the Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae), is connected with the transport of infested wood, in particular, railroad ties. Therefore, efficient treatment of infestations, especially along railroads, is imperative to prevent further termite damage and spread. Evaluation of treatment success hinges on the ability to assign infestation sites to colonies and compare colony identity before and after treatment. Because colonies of the Formosan subterranean termite can be headed by a pair of reproductives (simple families) or by multiple reproductives (extended families), the question arises whether the breeding system of a colony influences treatment success and whether treatment of an area might have an impact on the breeding system. We used microsatellite genotyping to compare colony affiliation and breeding systems of Formosan termites infesting the Riverfront Railroad, New Orleans, LA, before and after treatment with 0.5% noviflumuron. Before treatment, four colonies were simple families, and 11 colonies were extended families. A year after treatment began, all treated colonies had vanished and did not reappear during this study. One colony from an untreated monitoring station moved into a nearby station after treatment. Colonies that were detected after treatment consisted of 12 simple families and six extended families; extended families found after treatment contained a higher number of reproductive neotenics than the extended families found before treatment. Extended families were more likely than simple families to move into inground stations that had been previously occupied by termite colonies.