A phylogeny of Boronia (Rutaceae) is presented on the basis of maximum parsimony and Bayesian analyses of plastid (psbA–trnH, trnL–trnF, rbcL) and nuclear (ITS, ETS) markers. Analyses of either plastid or nuclear sequences recovered the same major clades, although with conflicts in resolution among them. The existing classification of Boronia is largely confirmed; sections Boronella, Pedunculatae and Valvatae are supported, and the monotypic sections Alatae and Imbricatae are isolated. Boronia corynophylla Paul G.Wilson is removed from section Algidae to the new section Corynophyllae. Boronia coriacea Paul G.Wilson is removed from section Boronia and placed, with B. inornata Turcz., in the new section Inornatae. Boronia humifusa Paul G.Wilson, B. ovata Lindl. and B. scabra Lindl. are placed in the new section Ovatae. Boronia koniambiensis is retained in section Boronella but placed in a new monotypic series. Section Boronia resolves into two clades that are confined to either south-eastern or south-western Australia, the latter containing three strongly to robustly supported subclades. An identified problem within section Boronia is the lack of morphological apomorphies to assist with formal classification. Despite this, a classification of four series, justified on the basis of the results of the molecular analysis, is proposed. Relationships among the 10 sections of Boronia remain poorly resolved apart from the sister relationships of sections Imbricatae with Pedunculatae, and, Alatae with Corynophyllae.