The cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) is a commonly known polyphagous pest in agricultural areas all over the world. It has been a major pest causing significant damages by reducing tomato fruit production and quality since 1913 in Turkey. The objective of the study was to evaluate genetic diversity and phylogenetic relationship of H. armigera based on mitochondrial COI gene. Infested tomatoes with H. armigera larvae were collected from Çanakkale province (14 location), Balıkesir (1 location) and Bursa (1 location) in August and September 2017 and 2018. Larvae representing for each location (n=3) were used for genomic DNA isolation. The partial COI gene (536 bp) was amplified and PCR products were sequenced directly. The numbers of haplotypes and mutations were estimated using the DnaSP. Genetic relationships between the population were evaluated using the UPGMA method in MEGA X program. As a result, we identified 13 haplotypes and 13 mutations in all tested 45 samples. Additionally, 9 private haplotypes were detected among H. armigera population. Analyses revealed that population of H. armigera sampled from different geographic location were established as two distinct groups. The first group comprised 12 haplotypes (Çanakkale and Balıkesir population) while the distinct second group consisted of only 1 haplotype (Bursa population). The presented study was the first attempt to detect molecular characterization and genetic characterization of cotton bollworm in Turkey.