Plastid (trnL intron and trnL-F spacer) and nuclear (ITS-1 and ITS-2 rDNA) regions were analyzed to infer the phylogeny and evaluate the classification of Rutaceae subfamilies Rutoideae and Toddalioideae. The inferred phylogeny lends support to merging these two subfamilies established by Engler based on different fruit types. Moreover, Phellodendron, Tetradium, Toddalia, and Zanthoxylum were resolved as a clade, supporting the proposal for a ‘proto-Rutaceae’ group. The molecular data also showed that members of Euodia sensu lato should be placed in three different genera: Tetradium, Euodia, and Melicope. The latter two genera are more closely related to Acronychia than they are to Tetradium. Except for the discrepancy in the position of Melicope vitiflora, the cladistic results are congruent with the morphological and biochemical interpretations made by two previous authors.