ABSTRACT Neoleucinodes elegantalis is an important tomato pest in Brazil, occurring throughout the country and resulting in economic losses in agriculture. In several species, biogeographic studies in Brazil indicate the structuring of populations, following the refuge model, with a split between the populations of the northeast and the southeast regions of Brazil. The objective of this work was to analyze the phylogeography of N. elegantalis in Brazil, understanding its population structure and the demographic patterns. Larvae were collected from eight locations throughout Brazil, and the mitochondrial cytochrome c oxidase subunit 1 gene was analyzed. A total of 628 bp in 51 individuals were obtained, showing 12 haplotypes with a haplotype diversity of 0.836. Spatial analysis of molecular variance (SAMOVA) and cluster analysis showed two populations, indicating population structuring between individuals from the northeast (population 1) and southeast (population 2) regions of Brazil. Phylogenetic analysis indicated that the clades corresponding to the groups defined by SAMOVA have a divergence time of 0.2–0.5 million years, suggesting isolation during climatic events and a separation of the two populations coinciding with the predicted refuges to the Atlantic forest.