Diatraea saccharalis(Fabricius) (Lepidoptera: Crambidae) is one of the major lepidopteran pests throughout the Western Hemisphere. In Argentina, it causes significant losses mainly in sugarcane (Saccharum officinarumL.) and corn (maize,Zea maysL.) (both Poaceae). Previous studies determined the existence of reproductive incompatibilities between populations from Buenos Aires and Tucumán from different host plants; however, the genetic basis of this incompatibility is still unknown. As the effectiveness of pest control programs mainly depends on strategies that minimize the risk of favoring insecticide‐resistant genotypes, estimating the level of mating between genotypes is important to monitor and manage resistance. The aim of this study was to characterize the genetic structure ofD. saccharalispopulations collected from various hosts and regions in Argentina, comparing with those from Brazil, through cytochrome c oxidase subunit I (COI) analysis and next‐generation sequencing (NGS). The COI analysis showed a haplotypic diversity of 0.8 and a nucleotide diversity of 0.0058. Analysis of molecular variance revealed greater variation within populations than among them. The 17 haplotypes detected were linked in a single parsimony network that did not reveal clusters based on geography or host plants. In total, 4549 single nucleotide polymorphism markers (SNPs) were obtained through NGS. Out of the 2349 outlier loci, 84 showed similarities with previously characterized proteins. The coefficient of inbreeding showed evidence of random matings as well as some degree of selection. The fixation index values showed high genetic variation between Argentinean and Brazilian populations; however, there was no clear trend based on distance or hosts. Similarly, the discriminant analysis of principal components revealed three separate groups: one Brazilian and two Argentinean. Results generated important clarification of the population genetic structure ofD. saccharalisin South America, which provides information about routes of dispersal and the development of suitable management strategies.