Abstract: Fifty-nine genotypes representing six genera of the True Citrus Fruit Trees Group (Aurantioideae, Rutaceae) were analyzed using AFLP technique to study their taxonomic and phylogenetic relationships. Fifteen primer combinations (out of 64 screened) were selected based on the polymorphism and quality of the bands produced by the primer and used in the present study. A total of 312 bands were obtained, of which 305 (97.8%) were polymorphic. The UPGMA tree of all genotypes was constructed based on the AFLP data using PAUP* beta version 4.0b8 software. Our AFLP molecular tree clearly confirms that the True Citrus Fruit Trees Group is monophyletic and supports the division of the group into genera mainly based on morphological characters, except that the genus Fortunella was nested within the genus Citrus cluster (as a monophyletic sub-branch). The subdivision of the genus Citrus into subgen. Papeda and subgen. Eucitrus as suggested by W. T. Swingle based on morphological characters and the point of view that C. medica, C. grandis and C. reticulata are the three basic species of the subgen. Eucitrus were also supported by our molecular data. In addition, contrary to the expectation based on morphological data, however, our molecular data demonstrated that C. ichangensis is more closely related to C. junos of the subgen. Eucitrus than to the C. hystrix of the subgen. Papeda. Furthermore, our study provided the first evidence that C. mangshanensis is basal to all the loose-skin citrus types. Finally, the taxonomic and phylogenetic relationships among the six genera and the important genotypes of the genus Citrus were dis-cussed in detail.