Oriental fruit fly, Bactrocera dorsalis, is one of the serious pests of fruit throughout the world. Two regional populations (Bangladeshi and Malaysia) were collected using methyl eugenol lure and one laboratory population was obtained from Thailand. Three populations were compared in cytochrome b (CYB) cytochrome oxidase I (COI) sequences. COI sequences were highly homologous. However, CYB sequences were polymorphic and used to discriminate these regional populations by a phylogenetic analysis. In CYB phylogeny analysis, Malaysia and Thailand populations were clustered and Bangladeshi population was separated