The taxonomy of Citrus is discussed in the light of the phylogeny of Citrus and allied genera inferred from the evolution of the segments trnL(UAA)-trnF(GAA) and trnT(UGU)-trnL(UAA) of the cpDNA. Twenty-eight species from twelve genera of subfamily Aurantioideae were sampled. Phylogenies constructed using maximum parsimony and neighbor-joining are well supported by high bootstrap values. The molecular data support a clade constituted by Citrus, Poncirus, Fortunella, and Microcitrus, but do not support an hypothesis of monophyly of Citrus due to the isolated position of C. medica. These results are congruent with an analysis of morphological evolution of diagnostic characters within the tribe Citreae. A more conservative position with a wider definition of Citrus to include all the cited relatives is intended to avoid great nomenclatural changes in such an economically important group.