Since its introduction from the United States in 1876, the invasive North American Eastern grey squirrel (Sciurus carolinensis) has contributed to the decline of the native Eurasian red squirrel (Sciurus vulgaris) in Britain. The aim of this study was to assess the overall impact of repeated control efforts carried out between 2011 and 2020 on the genetic diversity of the grey squirrel population in north Wales. This information can be used to inform future adaptive management plans, increasing the success of invasive species control efforts and enhancing red squirrel conservation efforts. Using a combination of mitochondrial DNA (mtDNA) and microsatellite DNA analysis, we found high genetic diversity in both marker types, with six diverse mtDNA haplotypes found and relatively high levels of nuclear genetic diversity, even after repeated culling efforts. We also found that repeated introductions from multiple locations in North America have generated a genetically diverse population in Britain today, compounding the management of this invasive species. Our results suggest that ongoing grey squirrel control efforts may not adequately reduce genetic diversity to a level where it contributes to a long-term population decline, and highlights the need to gather all available information, including historical and contemporary, to effectively create a plan for control efforts of invasive species.