The melon fly, Bactrocera cucurbitae Coquillett, is a species of fruit flies of significant agricultural interest. Of supposed Indian origin, the melon fly is now widely distributed throughout South East Asia up to China, while it has been recently eradicated from Japan. The population structure of seven geographic populations from coastal China, as well as samples from other regions of South East Asia and Japan, including lab colonies, have been studied using a 782 bp fragment of mitochondrial cytochrome oxidase I (COI) gene sequence. The observed genetic diversity was exceedingly low, considering the geographic scale of the sampling, and one single haplotype was found to be predominant from Sri Lanka to China. We confirm that Bactrocera cucurbitae exists in South East Asia as a single phyletic lineage, that Chinese populations are genetically uniform, and that no apparent genetic differentiation exists between these and three available Japanese melon fly sequences.