As currently circumscribed, Boronia (Rutaceae) is a large Australian genus of 148 species distributed in all states and mainland territories, and Boronella is confined to New Caledonia and contains ~four species. We present molecular phylogenetic analyses of these genera, based on chloroplast (trnL–trnF) and nuclear (ITS, ETS) DNA sequences, to assess their relationships and infrageneric classification. Analyses strongly support the monophyly of a Boronia+Boronella clade and that Boronella is nested within Boronia. They also support the monophyly of Boronella and Boronia sections Algidae, Valvatae and Cyanothamnus, and ser. Pedunculatae (sect. Boronia), but resolve sect. Boronia and ser. Boronia as polyphyletic. On the basis of these results, we propose a new classification wherein Boronella is transferred to Boronia and recognised at the rank of section, and a new name and two new combinations in Boronia are provided for the following three species: Boronia hartleyi Duretto & Bayly, Boronia pancheri (Baill.) Duretto & Bayly and Boronia parvifolia (Baker f.) Duretto & Bayly. A revised circumscription is presented for Boronia sect. Boronia, and Pedunculatae is elevated from a series to a section. The relationships and classification of some taxa require further clarification, either because of limited taxon sampling, or because some nodes in phylogenetic analyses are poorly resolved or supported.