Prostanthera is the largest genus of Lamiaceae in Australia and was last comprehensively revised in 1870. To test the classification, and the homology of the morphological characters on which it is based, we analysed nuclear (ETS) and chloroplast (trnT–F and ndhF–rpl32) sequence data for 71 species of Westringieae (Lamiaceae) in separate and combined datasets by using maximum-parsimony and Bayesian-inference methods. Results supported the monophyly of the Westringieae, but indicated that Prostanthera is paraphyletic with respect to Wrixonia, requiring the latter to be synonymised with the former. Although combinations of datasets provided some degree of infrageneric resolution within Prostanthera sensu lato, none of its sections or series could be recovered unambiguously. Prostanthera section Prostanthera and P. section Klanderia (regarded as entomophilous and ornithophilous, respectively) did not form a sister relationship, and neither could be unequivocally resolved as monophyletic. However, all species of P. section Klanderia nested within P. section Prostanthera raising the possibility that P. section Prostanthera is paraphyletic. Similarly, the phylogeny of Prostanthera based on molecular data could not be reconciled with the morphological definition of the traditionally recognised series. We recommend abandoning Bentham’s series as a means of organising morphological variation within the genus, but acknowledge that it is premature to discard Bentham’s sections. The evolutionary and systematic implications of the lack of congruence between our molecular phylogeny and morphologically defined subgeneric taxa are discussed.