Most of the edible Citrus species are believed to be of interspecific origin as a consequence of reticulate evolution. Garcia-Lor et al. conduct phylogenetic studies at intergeneric level (Citrinae, Rutaceae) and within the Citrus genus based on targeted gene nuclear DNA sequences, SSR and indel nuclear markers. They clarify the phylogenetic relationships between the ancestral ‘true citrus fruit trees’ species and find that they appear consistent with their original geographic distribution. In addition, the phylogenetic origin of the genes analysed is inferred for the cultivated Citrus species resulting from interspecific hybridization, giving new insights in particular into the origin of C. sinensis.