This study presents a molecular phylogeny of Zieria Sm., a genus of shrubs and small trees, with 59 species in Australia and one endemic to New Caledonia. The phylogeny is based on four cpDNA markers and 116 samples representing all species of Zieria except one, and the monotypic outgroup Neobyrnesia suberosa. The New Caledonian species, Z. chevalieri, was resolved as sister to a well supported clade of all Australian taxa. There was widespread incongruence between the cpDNA tree and species-level taxonomy, with 14 species shown as polyphyletic or paraphyletic. These included widespread species (e.g. Z. smithii and Z. arborescens, each falling in at least four well supported clades) and some with narrow geographic ranges (e.g. Z. alata and Z. oreocena). No species represented by three or more samples was resolved as monophyletic. We suggest that a combination of factors explains this incongruence, including regional cpDNA introgression (chloroplast capture), incomplete lineage sorting and inappropriate taxonomic boundaries. The cpDNA phylogeny provides useful insight into the evolution of Zieria but, because of its complexity, does not provide a clear basis for assessing phylogenetic relationships and monophyly of taxa. Better understanding of relationships, taxon limits and evolutionary processes in Zieria will require comparisons with nuclear DNA markers and critical assessment of morphological and genetic variation in widespread species.