BACKGROUND: A frequent goal of pest management strategies targeting social insects is total colony elimination. Insecticidal baits are highly effective at controlling social insect pests, although their ability to provide total colony elimination has only been well studied in a few species. Genetically testing colony elimination in many urban pest ants can be challenging due to indistinct colony boundaries observed in unicolonial, invasive species; however, some pest ants, such as the dark rover ant (Brachymyrmex patagonicus), maintain strict colony borders through aggression towards non-nestmates. Each of these distinct colonies can be identified using molecular markers, allowing for the tracking of individual colonies pre-and post-treatment to measure colony density. While counting the number of foraging workers to assess treatment efficacy may suffice in some cases, it offers little insight into the colony-level impacts of a treatment. RESULTS: Using microsatellite markers, distinct rover ant colonies were identified and tracked around residential structures before and after the application of an imidacloprid bait. The number of foraging ants at the treated structures was reduced by an average of 83.0% over a 28-day observation period. Baiting also significantly reduced the total number of colonies present. At the treatment structures, only ∼25% of the original colonies remained at the end of the study. Colonies with foraging trails <1.5 m from a bait station had a higher chance of being eliminated.CONCLUSION: Using insecticidal baits against B. patagonicus can be highly effective at colony elimination; however, with such small foraging ranges and high colony densities, proper placement is required to ensure enough bait is properly positioned to treat all colonies affecting a structure.