Sesamia nonagrioides (Lefèbvre) (Lepidoptera: Noctuidae), is a widespread insect pest in Africa, the Middle East, and Europe. However, its pest status varies across its distribution range. It is a major pest of maize in Europe and of sugarcane in Iran. In Africa, it is a major pest of maize in West Africa but not considered as a pest in East Africa. Recent surveys conducted in 2015 recorded S. nonagrioides to be a major pest of sugarcane in Ethiopia and reported the species for the first time in Botswana, outside its known geographic range. The genetic relationship of these records with the previously recorded population of S. nonagrioides was investigated using the cytochrome oxidase subunit I region of the mitochondrial genome. In total, 113 individuals across the geographic range of the species were analyzed and 63 haplotypes were identified. Phylogenetic analysis separated the populations into two clades with no distinct geographic distribution pattern. The genetic differentiation was also not associated with host plants and geographic distances. Results of the molecular analysis revealed the long-time establishment of S. nonagrioides population in Botswana and identified the newly recorded sugarcane population from Ethiopia as part of the wild host population in the country. The phylogeographic patterns observed among population of S. nonagrioides have probably been shaped by Pleistocene’s climatic oscillations and geographic range expansions from different refugia with secondary contact and admixture. Possible reasons for the host-plant expansion by the Ethiopian population are discussed.