Mosquitoes from the Culex pipiens complex are found worldwide and have been the focus of numerous studies due to their role as vectors of human pathogens. We investigated the population genetic structure of Cx. pipiens s.l. by analyzing single nucleotide polymorphisms (SNPs) and the COI gene, focusing on the genetic grouping signals of the ecotypes pipiens and molestus. Our analysis revealed no genetic association between the ecotypes and the SNPs, suggesting that the classification is based on ecological traits rather than genetic factors. Using data from 2,641 SNPs and 164 genotypes, our Bayesian clustering analysis categorized the populations into six distinct genetic groups, distinguishing the Rapa Nui island population from those on the American mainland. The estimated effective migration rates showed low levels of migration between island and continental populations, with significant migration occurring only among populations between 29° S and 33° S. Genetic differentiation between Rapa Nui island and the American continent was observed. In contrast, no significant differentiation was noted in other regions. The haplotype network suggests a possible migration pathway from that area of the South Pacific. In addition, demographic history analysis indicates a relatively recent founder effect of Cx. pipiens s.l. on the island. Geographic isolation and variations in genetic makeup can limit the spread of pathogens regionally and globally. However, these same factors can also promote specialization and enhance adaptation to new ecological niches, thereby improving the ability of pathogens to function as effective vectors in isolated environments.