[Objectives]  A method for rapid identification of fruit flies was developed and applied to identify the dominant species of these in China. [Methods]  Differences in the mitochondrial cytochrome oxidase subunit Ⅰ factor (mtCOⅠ) gene sequences of three fruit fly species; Bactrocera cucurbitae (Coquillett), Bactrocera tau Walker and Bactrocera dorsalis (Hendel), and differences in mtCOⅠ gene fragment size after enzyme digestion (SapⅠ, BsmⅠ and SacⅠ), allowed these three species of fruit flies to be rapidly identified. This technique was further applied to the identification of 21 fruit fly larvae samples from 7 kinds of vegetable and 2 kinds of fruit crops from 7 provinces and 11 cities in China. [Results]  Identification methodology based on PCR-RFLP was successfully established and used to identify sample of fruit fly larvae collected in the field. The results show that the main fruit fly pest of melons and vegetables in the Hubei, Hunan and Zhejiang regions is B. tau; whereas in Guangdong, Guangxi and Hainan the main fruit flies are B. cucurbitae, with some B. tau and B. cucurbitae. The main fruit fly pest of pitaya and mango crops in Yunnan is B. dorsalis. [Conclusion]  The PCR-RFLP method developed for the identification of B. cucurbitae, B. tau and B. dorsalis is not affected by the developmental stage of fruit flies, and is relatively inexpensive, efficient, fast and repeatable. It is especially suitable, therefore, for identifying fruit fly larvae. Using this method to identify samples of larvae from different provinces and cities suggests that B. cucurbitae may be gradually spreading northwards.