Fruit flies (Diptera: Tephritidae) are significant insect pests of many commercially important fruits and vegetables. Therefore, rapid and accurate species identification methods are required for the regulation, management and quarantine of these pests. In this study, we examined the efficiency of mitochondrial cytochrome c oxidase I sequences for species identification of fruit flies in Thailand. Data analyses based on 42 fruit fly taxa revealed moderate performance of this genetic marker. There were 14 taxa that have no barcode gap and thus could not be identified unambiguously to species by this methodology. Taxonomic uncertainty, inadequate variation of the marker and misidentifications of specimens deposited in the public database are the most likely factors explaining unsuccessful identification. DNA barcodes also revealed cryptic diversity in five taxa (Bactrocera caudata, B. tuberculata, B. infesta, Zeugodacus isolatus, Carpomya vesuviana). These species require further taxonomic investigation of if they are different cryptic taxa or are indications of geographic structuring of within single species.

果蝇（双翅目：蝇科）是许多商业上重要的水果和蔬菜的重要害虫。因此，需要快速，准确的物种识别方法来控制，管理和隔离这些害虫。在这项研究中，我们检查了线粒体细胞色素c的效率氧化酶I序列用于泰国果蝇的物种鉴定。基于42个果蝇类群的数据分析表明，该遗传标记的表现中等。有14个没有条形码间隙的类群，因此无法通过这种方法明确地识别出物种。分类学上的不确定性，标记的不充分变化以及公共数据库中存放的标本的错误识别是最可能导致识别失败的因素。DNA条码还揭示了5个类群（拟杆菌（Bactrocera caudata），结核杆菌（B. tuberculata），侵染芽孢杆菌（B. infesta），异毛肠球菌（Zeugodacus isolatus），vespiana）。这些物种需要进一步的分类学研究，以了解它们是否是不同的隐性分类单元，或者是否表明单个物种内部的地理结构。