Spyridium parvifolium is a widespread and morphologically variable shrub from south-eastern Australia. Several varieties have been recognised and there is disagreement on the accepted taxonomy between Australian states. This study investigated the phylogeography of the species and assessed genetic distinctiveness of its morphological variants. Nuclear ribosomal DNA and complete chloroplast genomes from seventy-three samples of S. parvifolium and seven samples from closely related species were sequenced and analysed using both Bayesian and Maximum Likelihood phylogenetic methods. The results showed incongruence in the placement of several associated taxa (S. cinereum, S. obcordatum and S. daltonii), plausibly due to long-branch attraction, introgression or incomplete lineage sorting. Spyridium parvifolium was resolved as paraphyletic in both phylogenies, with accessions from west of the Murray Darling Depression divergent from those east of the Depression. We found evidence of isolation within S. parvifolium on the inland side of the Great Dividing Range, and recent gene-flow across Bass Strait. The variants of S. parvifolium were not supported as genetically distinct and, with the prevalence of several variants at single sites and morphological intergrades between variants, we conclude that the taxon is a single, morphologically variable species and that no infraspecific classification is warranted.