The fruit fly genus Ceratitis is mainly an Afrotropical taxon which includes several pest species of agricultural importance. The 89 currently recognized species are arranged in six subgenera: Ceratitis s.s., Pardalaspis, Ceratalaspis, Pterandrus and the monotypic Hoplolophomyia and Acropteromma. Two non-monotypic subgenera lack evidence for monophyly, and the interrelationships between and within the subgenera are poorly understood. A cladistic analysis was performed, based on a suite of 95 characters from adult morphology and host plant specificity for all species within the genus. The analysis strongly supports the monophyly of the subgenera Pardalaspis and Ceratitis s.s. whereas the monophyly of the subgenus Pterandrus is poorly supported and the subgenus Ceratalaspis clearly is not monophyletic. Species groups within Pterandrus and Ceratalaspis are recognized and their interrelationships are discussed. The monotypic Hoplolophomyia belongs to the argenteobrunnea species group of Ceratalaspis whereas the position of Acropteromma probably is outside the genus Ceratitis.