Discrimination of particular species within the species complexes of tephritid fruit flies is a very challenging task. In this fruit-fly family, several complexes of cryptic species have been reported, including the African cryptic species complex (FAR complex). Cuticular hydrocarbons (CHCs) appear to be an excellent tool for chemotaxonomical discrimination of these cryptic species. In the present study, CHC profiles have been used to discriminate among three important agricultural pests from the FAR complex, Ceratitis fasciventris, Ceratitis anonae and Ceratitis rosa. Hexane body surface extracts of mature males and females were analyzed by two-dimensional gas chromatography with mass spectrometric detection and differences in CHC profiles between species and sexes tested through multivariate statistics and compared with species identification by means of microsatellite markers. Quantitative as well as qualitative CHC profile differences between sexes and species are reported. The CHC profiles consisted of a mixture of linear, internally methyl-branched and mono-, di- and tri-unsaturated alkanes. Twelve compounds were pinpointed as potential chemotaxonomical markers. The present study shows that presence or absence of particular CHCs might be used in the chemical diagnosis of the FAR complex. Moreover, our results represent an important first step in the development of a useful chemotaxonomic tool for cryptic species identification of these important agricultural pests.