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Background: Spodoptera frugiperda is a destructive pest that often imposes difficult management due to its high polyphagy and rapid insecticide resistance evolution. Knowledge of species diversification, population structure, and host preference can aid efforts to manage pest populations. Here, we investigated the patterns of hybridization, genetic structure, and gene flow in S. frugiperda populations, discussing how we can apply this knowledge to insect resistance management programs in South America., Results: The corn-strain CS-h2 of S. frugiperda was the most frequent haplotype in all sampled populations. Spodoptera frugiperda populations are experiencing demographic expansion, and the ecoregions partially explain the genetic structure and not strains. We did not find a correlation between gene flow and susceptibility levels to flubendiamide and lufenuron insecticides, but populations with high LC 50 sent a great number of migrants to all other locations, maintaining resistance alleles in the geographic range., Conclusion: High levels of population admixture, including between corn- and rice-strains, were found in sampled populations. We showed that S. frugiperda immigrants will not necessarily cause an increase in LC 50 upon arrival in a new location but will assure the constant presence of resistance alleles in the area. Increases in LC 50 largely depend on the local pesticide management adopted in the areas. Our results indicate that pesticide resistance management must be adopted on a local or small regional scale. © 2019 Society of Chemical Industry., (© 2019 Society of Chemical Industry.)