Along with the increasingly frequent and complex international trade activity and the import-export trade of many products such as fruits and vegetables, the probability of the spread of fruit fly pests increases. This directly threatens the fruit and vegetable planting industry and agriculture production safety, making it an important quarantine problem. Therefore, the accurate and quick identification of fruit flies is receiving great attention by the quarantine services all over the world. This article mainly describes the principle and the advantages, disadvantages and the research progress of the molecular biology-based technology in fruit fly identification. Meanwhile, according to the existing data of BOLD Systems summarized the types of DNA barcoding of fruit fly, published records and the species of fruit fly involved until October 22, 2014. The conclusion is that there are 7 DNA barcoding, they are COⅠ-5P, COⅠ-3P, COⅡ, COⅢ, CYTB, atp6, 28S, but mainly based COⅠ markers, with the number of published records was 4540, it was 113.5 times of the other five kinds of DNA markers; the species of fruit fly researched by COⅠ-5P marker were 315, while COⅠ-3P marker were 116, currently studied more for Bactrocera, Dacus and Ceratitis. This article has the important theoretical significance and reference basis on how to choose the molecular biology technology to identify fruit fly.