The study was conducted to determine the genetic structure of Lobesia botrana (Denis and Schiffermuller 1775) (Lepidoptera: Tortricidae) populations from South of Turkey by molecular methods. Mitochondrial DNA cytochrome oxidase gene was used for phylogenetic and population genetic analyses comparing specimens from Mediterranean (MED-TR) and South East Anatolia (SEA-TR) Regions of Turkey with reference sequences from the Middle East and Europe deposited in GenBank. The Turkish specimens were allocated to seven haplotypes. Binary genetic distance between MED-TR and SEA-TR was above 0.6, whereas, between the Middle East and MED-TR was only 0.034. Gene flow was infinite between MED-TR and the Middle East, but was 0.23 between SEA-TR and the Middle East as the lowest. The two common haplotypes from Turkey were placed in two clades on the phylogenetic tree, separated with a bootstrap value of 100. The common haplotype from MED-TR clustered on the same branch at the tree with the sequences from Israel and Greece, whereas, the common haplotype from SEA-TR was close to European haplotypes, with this separation supported by haplotype network analysis. Overall, the results showed that L. botrana populations in these two adjacent geographic regions of Turkey consist mostly of two genetically different haplotypes. This could be a consequence of the cultivars grown, the production methods and/or the climatic conditions in SEA-TR. However, the most prevalent haplotype in MED-TR, with a predominantly Mediterranean climate, is likely to be prevalent in other Mediterranean Basin countries with a similar climate.