Insecticide resistance amongst vector populations is a major challenge, exacerbated by the continued use of the same active ingredients. The present study assessed the impact of long-lasting insecticidal nets (LLINs) bi-treated with chlorfenapyr-alphacypermethrin (PY-CFP LLIN) or pyriproxyfen-alphacypermethrin (PY-PPF LLIN) on the genetic structure of resistant populations of Anopheles gambiae in 60 clusters divided into three arms from three districts in southern Benin.