The utility of the cytochrome oxidase I gene barcode region for diagnosis of the Mediterranean fruit fly, Ceratitis capitata (Weidemann), is evaluated using African fruit fly collections. The method fails to discern C. capitata from its close relative Ceratitis caetrata Munro, based on genetic distances, parsimony networks, or nucleotide diagnostic characters observed in the DNA barcode sequences. When treated as a single taxon, it is possible to discern the C. capitata C. caetrata lineage from other Ceratitis species. Levels of intraspecific diversity vary within the genus Ceratitis and multiple copies of the mitochondrial gene are reported for Ceratitis cosyra (Walker). The DNA barcoding method based on genetic distance is compared with a molecular identification method using restriction fragment length polymorphism. The DNA barcode and restriction fragment-length polymorphism methods provide similar identification results, but the DNA sequence information is more suitable for quantitative analysis of the information.