Prostanthera gilesii Althofer ex. B.J.Conn & T.C.Wilson is a critically endangered species from the Central Tablelands of New South Wales. A conservation management strategy is currently underway for this species, whose phylogenetic affinities are not known. Morphologically, P. gilesii resembles P. phylicifolia F.Muell. and a population of uncertain identity from Evans Crown Nature Reserve in the Central Tablelands of New South Wales known as P. sp. Evans Crown (G.M.Taseski NSW1055966). The taxonomy of P. phylicifolia, however, is unclear. Prostanthera phylicifolia was described from populations in the Victorian Alps and Monaro; however, populations spanning from Victoria to southern Queensland have been variously identified as either P. phylicifolia or P. scutellarioides (R.Br.) Briq. despite substantial geographic disjunctions and morphological dissimilarity. To examine the relationship between populations identified as P. phylicifolia, P. gilesii and P. sp. Evans Crown, nuclear (external transcribed spacer, ETS) and chloroplast (trnH-psbA intergenic spacer) regions were sequenced and combined with an existing Prostanthera dataset and analysed with maximum-likelihood and Bayesian-inference methods. Prostanthera gilesii and P. sp. Evans Crown were recovered as sister taxa within a clade consisting of populations morphologically similar to the type of P. phylicifolia from the Victorian Alps and Snowy Mountains, Monaro and Southern Tablelands of New South Wales. Populations from northern New South Wales and southern Queensland identified as P. phylicifolia or P. scutellarioides were recovered as an assemblage of unrelated clades. The molecular phylogeny supports P. gilesii and P. phylicifolia as closely related as hypothesised based on morphology and supports P. sp. Evans Crown as a population which requires additional study to assess its taxonomic status.