The long-term efficacy of vector control programs is seriously hampered by the evolution of insecticide resistance. In this scenario, assessing the distribution, frequency, and drivers of resistance spread is crucial to planning effective control programs. Here, we addressed these issues in the mosquito Culex pipiens, focusing on the Emilia-Romagna region (Italy), a known hotspot of diflubenzuron (DFB) resistance. First, Cx. pipiens larvae were screened for point mutations conferring DFB resistance to capture the distribution and frequency of resistance-associated alleles across the region. To this end, a fragment of the chitin synthase 1 gene spanning the mutated site was sequenced. Then, by using population genomics, we investigated the vector population structure in this area. Our findings revealed that resistance-associated alleles maintain a focal geographic distribution in the region, with higher mutation frequencies in the central-eastern than in the western provinces. Also, we observed that the populations of Cx. pipiens are a highly homogeneous gene pool and can be interconnected across the region, highlighting the risk of resistance alleles spread across Emilia-Romagna. Overall, this study stresses the importance of systematically surveying resistance-associated alleles and their integration with population genomic data to gain relevant information for resistance management.