The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an important invasive pest species in the United States causing over 1 billion dollars worth of damage to wooden structures annually. Due to the cryptic life of subterranean termites, their colony organization cannot be directly observed, but needs to be inferred from the genetic structure. We investigated the population dynamics and genetic structure of C. formosanus around the Wildlife and Fisheries building, New Orleans, to identify the number and social structure of colonies and investigate the source of reinfestation. From 2001 to 2004 workers were collected from infested inground stations on a monthly basis. Microsatellite markers were applied to assign termites to colonies through diagnostic bands and genotypic frequencies. At least 16 colonies were identified in the perimeter of this building over the four years. Colony breeding structure was inferred from worker genotypes and from comparing estimates of F-statistics and the coefficient of relatedness to expected values based on previous computer simulations of subterranean termite breeding systems. Only about 20% of the colonies were simple families (headed by a single pair), while 80% were extended families (headed by multiple reproductives). Over time the population shifted entirely towards extended family colonies. None of the reinfestations over time belonged to the colony previously found in the inground station. The high colony density and the high reinfestation rate we have found in this study show the immense termite pressure in this area.