Several different taxa within the genera Dacus and Ceratitis (Diptera: Tephritidae) are important agricultural pests in Sub-Saharan Africa. Although the status of many of these taxa as distinct species and their phylogenetic relationships is unclear, it is clear that these pests use a wide range of host plants and are highly invasive. The great potential for economic damage inflicted by these pests requires the ability to make accurate and reliable taxonomic identification of specimens. However, many limitations and uncertainties are encountered when these species are examined using traditional approaches based on morphological identification techniques. We describe here the amplification and analysis of DNA sequences from the mitochondrial cytochrome oxidase II (COII)-tRNA_lys-tRNAAsp genes from individuals of various Dacus and Ceratitis species and populations from Sub-Saharan Africa. The variation detected in the DNA sequences of these individuals is used both for clarification of their taxonomic status and the analysis of phylogenetic relationships of these taxa.