We investigated the use of termite baiting, a proven system of targeted colony elimination, in an overall area-wide control strategy against subterranean termites. At two field sites, we used microsatellite markers to estimate the total number of Reticulitermes colonies, their spatial partitioning, and breeding structure. Termite pressure was recorded for two years before and after the introduction of Trelona^® (active ingredient novaluron) to a large area of one of the sites. Roughly 70% of the colonies in the treatment site that were present at the time of baiting were not found in the site within two months after the introduction of novaluron. Feeding activity of the remaining colonies subsequently ceased over time and new invading colonies were unable to establish within this site. Our study provides novel field data on the efficacy of novaluron in colony elimination of Reticulitermes flavipes, as well as evidence that an area-wide baiting program is feasible to maintain a termite-free area within its native range.