Termite pressure caused by the invasive pest species Coptotermes formosanus Shiraki is extremely high along the Riverfront Railroad in New Orleans, La., and the economic impact in the area is severe. We investigated the colony dynamics of this termite along the railroad and levee in relation to treatment. Termites were collected from Sentricon stations before and after treatment with 0.5% Noviflumuron bait. Due to the cryptic nature of subterranean termites, molecular techniques are needed to describe their colony structure. Microsatellite genotyping allowed us to compare the number and spatial extent of colonies, and their social structure (headed by a single pair or multiple reproductives). Comparing the multilocus genetic profiles of each pretreatment colony and its corresponding invader allowed us to determine if, after treatment, termite colonies are eliminated, or if they return to the same bait station. In most cases, the termites found after treatment were significantly genetically differentiated from termites collected at the same station before treatment. This suggests successful colony elimination. Through further comparison we will be able to track the sources of these new infestations and also assess whether colony breeding system affects treatment success and vice versa.