The current classification of African tephritids is the interim result of a continuous process of minor and major changes that, in the last 20 years, has resulted in the description of more than 60 new species from the seven tephritid genera of main economic relevance in Africa (Bactrocera, Capparimyia, Ceratitis, Dacus, Neoceratitis, Trirhithrum and Zeugodacus). In this context of dynamic change, rapid and accurate fruit fly identification is critical, particularly with respect to the early detection of pest invasions. Valuable resources for fruit fly identification include: the tephritid reference collections and repositories distributed within and outside the African continent; publicly available online databases; and the single- and multi-entry keys for the morphological identification of African tephritids. Identification through DNA barcoding represents a cost effective tool for the molecular diagnosis of African fruit flies and it has proved particularly useful for the identification of immature stages, of damaged specimens and of incomplete specimens. The molecular diagnosis of tephritids also represents a partial solution to the gradual loss of taxonomical expertise on this and other insect groups. In this chapter the advantages and limitations of the available identification tools and resources are discussed.